Thermal cycling method

ABSTRACT

This invention provides a method for carrying out nucleic acid amplification reactions involving heating and cooling of samples in sample vessels utilizing a heat block comprising a liquid. The method can be used to perform multiple nucleic acid amplification reactions simultaneously in which each of the reactions is performed so as to have temperature profiles. The apparatus can be used for performing PCR, and real time PCR in particular, with control and uniformity.

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No.11/750,326, filed May 17, 2007, which claims the benefit of U.S.Provisional Applications No. 60/801,178 filed May 17, 2006, 60/832,492,filed Jul. 21, 2006, 60/873,084 filed Dec. 6, 2006, and 60/873,172 filedDec. 6, 2006, which applications are incorporated herein by reference.

BACKGROUND OF THE INVENTION

Invented in 1983 by Kary Mullis, PCR is recognized as one of the mostimportant scientific developments of the twentieth century. PCR hasrevolutionized molecular biology through vastly extending the capabilityto identify and reproduce genetic materials such as DNA. Nowadays PCR isroutinely practiced in medical and biological research laboratories fora variety of tasks, such as the detection of hereditary diseases, theidentification of genetic fingerprints, the diagnosis of infectiousdiseases, the cloning of genes, paternity testing, and DNA computing.The method has been automated through the use of thermal stable DNApolymerases and a machine commonly referred to as “thermal cycler.”

The conventional thermal cycler has several intrinsic limitations.Typically a conventional thermal cycler contains a metal heating blockto carry out the thermal cycling of reaction samples. Because theinstrument has a large thermal mass and the sample vessels have low heatconductivity, cycling the required levels of temperature is inefficient.The ramp time of the conventional thermal cycler is generally not rapidenough and inevitably results in undesired non-specific amplification ofthe target sequences. The suboptimal performance of a conventionalthermal cycler is also due to the lack of thermal uniformity widelyacknowledged in the art. Furthermore, the conventional real-time thermalcycler system carries optical detection components that are bulky andexpensive. Mitsuhashi et al. (U.S. Pat. No. 6,533,255) discloses aliquid metal PCR thermal cycler.

There thus remains a considerable need for an alternative thermal cyclerdesign. A desirable device would allow (a) rapid and uniform transfer ofheat to effect a more specific amplification reaction of nucleic acids;and/or (b) real-time monitoring of the progress of the amplificationreaction in real time. The present invention satisfies these needs andprovides related advantages as well.

SUMMARY OF THE INVENTION

In one aspect this invention provides a method of performing PCRcomprising: a) performing PCR in a sample vessel and generating a signalin the sample vessel indicating the course of the PCR, whereinsubstantially all said signal is reflected back into said sample vessel,wherein substantially all the signal is detected from said sample vesselfrom a discrete location; and b) measuring the signal emitted from thediscrete location of the sample vessel. In one embodiment the methodcomprises measuring the signal over a plurality of PCR cycles in realtime. In another embodiment the sample vessel comprises a walltransparent to the signal and at least part of the wall is immersed in aliquid composition that reflects substantially all the signal strikingthe liquid composition. In another embodiment the liquid compositioncomprises a metal or metal alloy. In another embodiment the signal isgenerated by a label or dye. In another embodiment said sample vesselcomprises a material that reflects substantially all said signal in saidsample in another embodiment said sample vessel is comprised of a metal.In another embodiment said sample vessel comprises a reflectivematerial. In another embodiment said sample vessel is separated fromsaid liquid composition by a receptacle.

In another aspect this invention provides a method of performing PCRcomprising: a) performing PCR of a target nucleotide sequence in areaction mixture under conditions wherein; (i) the rate of temperaturechange between primer extension and duplex dissociation and betweenprimer annealing and primer extension is more than 10.5° C. per second(ii) said PCR is conducted in a heat block comprising sample vessels,comprising temperature variance of less than 0.5° C. within a samplevessel; and b) monitoring amplification of the target nucleotidesequence in real time. In one embodiment said heat block comprises aliquid composition. In another embodiment said method of performing PCRfurther comprises a temperature variance of less than 0.5° C. asmeasured between two or more wells in said heat block. In anotherembodiment said temperature variance is 0.01° C. as measured between twoor more wells in said heat block. In another embodiment said heat blockis a swap block. In another embodiment the rate of temperature change iseffected by: (1) putting a sample vessel containing the reaction mixturein thermal contact with a liquid composition having a heat transfercoefficient of at least 0.1 W/m*K; wherein the temperature of the liquidcomposition controls the temperature of the reaction mixture. In anotherembodiment the temperature uniformity is maintained by inducing movementof the liquid composition.

In another aspect this invention provides a method of performing PCRcomprising: conducting PCR in a thermal cycler which modulates sampletemperature by more than 5° C. per second; wherein said thermal cyclertemperature is regulated by a liquid composition in heat block with aliquid tight seal; wherein said liquid composition comprises a heattransfer coefficient of at least 0.1 W/m*K. In one embodiment saidthermal cycler provides ramp rates of at least about 10° C. per second.In another embodiment said thermal cycler provides well-to-well andsample temperature uniformity of at least about 0.01 to 0.1° C. Inanother embodiment said heat block has a temperature variance is 0.01°C. as measured between two or more wells in said heat block. In anotherembodiment said liquid composition is contained within a heat block. Inanother embodiment said heat block is a swap block.

In another aspect this invention provides a method of performing PCRcomprising; conducting PCR in a thermal cycler which modulates sampletemperature sufficiently to allow detecting amplification in real timeat a signal index of at least 3, wherein said detection is via anon-specific nucleic acid label, wherein said thermal cycler modulatessample temperature by more than 10° C. per second.

In another aspect this invention provides a method for performingreal-time PCR comprising: a) performing a PCR reaction of a targetnucleotide sequence in a reaction mixture under conditions wherein therate of temperature change between primer extension and duplexdissociation and between primer annealing and primer extension in thereaction mixture is at least 5° C. per second, wherein said PCR reactionis in thermal contact with a liquid composition having heat transfercoefficient of at least 0.1 W/m*K; and b) monitoring the PCR in realtime. In one embodiment said monitoring comprises: a) performing PCR ina sample vessel and generating signal in the sample vessel indicatingthe course of the PCR, wherein the signal is emitted from the samplevessel substantially from a discrete location; and b) measuring thesignal emitted from the discrete location of the sample vessel. Inanother embodiment said rate of temperature increase in the reactionmixture is at least 40° C. per second. In another embodiment saidtemperature change is regulated by a Peltier element.

In another aspect this invention provides a method for performingreal-time PCR comprising: a) cycling the temperature of the PCR reactionmixture between temperatures for duplex dissociation, primer annealingand primer extension for a plurality of cycles, wherein each cycle is nomore than five seconds; wherein said temperatures are modulated by aliquid composition sealed in a thermal cycler; b) monitoring the courseof PCR in the sample vessel in real time over a plurality of cycles. Inone embodiment the method further comprises before step (a): placing aclosed end of a sample vessel containing the PCR reaction mixture intothermal contact with a liquid composition that is liquid above 60° C.and that has a heat transfer coefficient of at least 0.1 W/m*K, wherebythe temperature of the liquid composition controls the temperature ofthe PCR reaction mixture 30. In another embodiment said liquidcomposition reflects substantially all light inside the sample vessel.In another embodiment said monitoring is performed by measuring signalemitted from the top or bottom of the sample vessel. In anotherembodiment each cycle is no more than three seconds. In anotherembodiment said sample vessel comprises a reflective surface. In anotherembodiment said sample vessel is further covered with a cap. In anotherembodiment said cap is capable of absorbing heat from or being cooled bysaid liquid composition.

In another aspect this invention provides a method for conducting realtime PCR comprising providing a thermal cycler comprising a liquidcomposition in thermal contact with PCR sample vessels; wherein saidliquid composition modulates in temperature thus regulating reactiontemperatures in the sample vessels, wherein a detectable signal isemitted from said sample vessels; and detecting said signal via anoptical assembly comprising a light emitter and optical detector. In oneembodiment said optical assembly comprises a pin photodiode CCD imager,a CMOS imager, a line scanner, a photodiode, a phototransistor, aphotomultiplier or an avalanche photodiode. In another embodiment saidsample vessel is further covered with a cap. In another embodiment saidcap is capable of absorbing heat from or being cooled by said liquidcomposition.

In another aspect this invention provides an apparatus comprising: a) atemperature control assembly comprising a container containing a liquidcomposition that is liquid above 60° C. and that has a thermalconductivity of at least 0.1 W/m*K, said container having at least oneaperture, each aperture adapted to receive a closed end of an samplevessel, wherein a sample vessel received into the aperture is placed inthermal contact with the liquid composition whereby the temperature ofthe liquid composition controls the temperature of a liquid sample inthe sample vessel and wherein the liquid composition is capable ofreflecting substantially all light inside the sample vessel; b) anoptical assembly capable of detecting said light inside the samplevessel from a discrete location on said sample vessel; and c) a controlassembly that controls the temperature of the liquid composition and theoperation of the optical assembly. In one embodiment the liquidcomposition comprises gallium, a gallium-indium alloy or alloycomprising gallium, indium, rhodium, silver, zinc, tin or stannous. Inanother embodiment said temperature controller comprises a Peltierelement. In another embodiment said temperature controller comprisesresistive wire in thermal contact with the liquid composition. Inanother embodiment said temperature controller comprises means to cyclethe temperature of the liquid composition between temperatures forduplex dissociation, primer annealing and primer extension appropriatefor PCR. In another embodiment said thermal cycler further comprisesmeans for circulating current in the liquid composition. In anotherembodiment said optical assembly comprises a light emitter and opticaldetector. In another embodiment said apparatus further comprises asample preparation station comprising means to add reagents to samplevessels. In another embodiment said apparatus further comprises a meansfor moving the sample vessels into the apertures. In another embodimentsaid apparatus further comprises a digital computer that controls thethermal cycler, the optical assembly and the sample preparation station.

In another aspect this invention provides a system for performing realtime PCR comprising: a) a thermal cycler comprising a liquid compositionand means to engage a sample vessel and put said vessel in thermalcontact with the composition; and b) an optical assembly comprising alight emitter and optical detector that directs light into an engagedsample vessel and detects light emitted from an engaged sample vessel.In one embodiment said liquid composition comprises a metal or metalalloy. In another embodiment said liquid composition comprises gallium.In another embodiment said signals emitted are from a removable cap ofsaid sample vessel. In another embodiment said liquid composition isseparated from said sample vessel by a receptacle. In another embodimentsaid receptacle is transparent or translucent. In another embodimentsaid system comprises a Peltier element. In another embodiment saidthermal cycler farther comprises a motor operatively connected to a fanand stir bar. In another embodiment said fan and stir bar are connectedcoaxially to said motor. In another embodiment said thermal cyclerfurther comprises a resistive wire for thermal regulation of said liquidcomposition. In another embodiment said liquid composition is sealed ina closed barrier, wherein said barrier comprises a surface withreceptacles into which said sample vessels are placed. In anotherembodiment said liquid composition directly contacts said samplevessels. In another embodiment said optical assembly comprises a PINphotodiode, CCD imager, a CMOS imager, a line scanner, a photodiode, aphototransistor, a photomultiplier or an avalanche photodiode.

In another aspect this invention provides an apparatus comprising a) aheat sink; b) a heating component in thermal contact with the heat sink;c) a barrier comprising a wall having a top and bottom surfaces, whereinthe bottom surface is sealed to the said heating component wherein thesealed barrier and said heating component form a container containing aliquid composition; d) a first piece comprising a plurality of wells,wherein the first piece is sealed to the top surface of the barrier andthe wells extend into the container; e) a second piece comprising aplurality of sample vessels, each with an open end, wherein the samplevessels are removably inserted into the wells; f) a third piececomprising a plurality of extrusions, wherein the extrusions areremovably inserted into the open ends of the sample vessels. In oneembodiment said liquid composition comprises a metal that is liquidabove 60° C. and that has a heat transfer coefficient of at least 0.1W/m*K. In another embodiment said liquid metal is capable of increasingin volume by about 0.1 to 6.0%. In another embodiment said capable of anincrease in temperatures is more than 10.5° C./second. In anotherembodiment said well is adapted to be flexible so that said well iscapable of forming a thermal or optical contact with said samplevessels. In another embodiment said adapting comprises utilizing ageometric configuration and or deformable material in said well. Inanother embodiment said geometric configuration is polygonal, ellipticalor circular. In another embodiment said wells are immersed in saidliquid composition to an initial level. In another embodiment saidextrusion extends to above, at or below said initial level. In anotherembodiment said third piece is capable of absorbing heat from or beingcooled by said liquid composition. In another embodiment said wells ofthe first piece are transparent and flexible, and the sample vessels ofthe second piece are transparent, whereby increased pressure on saidwells places said liquid in said container in thermal and opticalcontact with a sample in said sample vessel. In another embodiment saidextrusions of the third piece are transparent. In another embodimentsaid barrier is sealed to each of a heat spreader and the first piecethrough a gasket. In another embodiment said first piece or second piececomprises a reflective surface. In another embodiment the barrier issealed to each of a heat spreader and the first piece with a fastener.In another embodiment said apparatus further comprises a heat spreaderin contact with said heating component. In another embodiment saidheating component is a Peltier, wire elements or a combination thereof.In another embodiment said apparatus further comprises a second heatingcomponent, wherein said barrier is disposed between said heatingcomponent and said second heating component. In another embodiment saidplurality of wells comprise 4, 8, 16, 32, 48, 96, 196, 384 or 1536wells. In another embodiment said apparatus further comprises a fan andstir bar, wherein optionally said fan and stir bar are operativelyconnected to a single motor. In another embodiment said apparatus ispowered by a battery. In another embodiment said fan is turned on andoff automatically by a controller component operatively connected tosaid apparatus. In another embodiment said apparatus further comprises ametal heat spreader. In another embodiment said spreader comprisescopper. In another embodiment said heating component is configured forgradient PCR.

In another aspect this invention provides a continuous flow PCR systemcomprising a sample preparation module; thermal cycler, wherein saidthermal cycler comprises a liquid composition for modulating temperaturein said sample; and an optical assembly for detecting an emission signalfrom said sample. In one embodiment said system further comprises asampler and a waste collection.

INCORPORATION BY REFERENCE

All publications and patent applications mentioned in this specificationare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1 illustrates a thermal cycler body for use with a liquidcomposition swap heat block. (A) A 48-well “swap block” device isdepicted on sliding rails. The block is slid out, loaded with a samplevessel well plate and sample well plate caps, and then slid into thermalcycler body and the door is closed. The thermal cycler body may comprisean optical assembly, control electronics, fans, and optionally a powersupply. (B) Thermal cycler body with “swap block” slid into theoperating position.

FIG. 2 illustrates a swap block embodiment comprising 48 sample vesselwells. In this embodiment the swap block comprises, from top to bottom:a single piece serving as 48 transparent caps; a single piece creating48 sample vessel wells; a single receptacle piece with 48 reaction well,which forms the ceiling of liquid metal container; a plastic housingforming walls of liquid metal container; a metal plate forming bottomfloor of liquid metal container; a Peltier device(s) for heating andcooling; and a metal heat sink for removing heat from Peltier device(s).

FIG. 3 illustrates an exploded view of a swap block embodiment. In thisembodiment the swap block comprises, from top to bottom: a single pieceserving as 48 transparent lids, a single piece serving as 48 transparentcaps; a single piece creating 48 sample vessel wells; a singlereceptacle piece with 48 reaction well; a rubber or plastic gasket orring that forms a liquid tight seal to contain the liquid metal; aplastic housing forming walls of liquid metal container; a rubber orplastic gasket or ring that forms a liquid tight seal to contain theliquid metal; and optionally a metal plate forming bottom floor ofliquid metal chamber; a Peltier device(s) for heating and cooling; and ametal heat sink for removing heat from Peltier device(s).

FIG. 4 illustrates a second view of a swap block embodiment. In thisembodiment the swap block comprises, from top to bottom: a single pieceserving as 48 transparent caps; a single piece creating 48 sample vesselwells; a single receptacle piece with 48 reaction well; a rubber orplastic gasket or ring that forms a liquid tight seal to contain theliquid metal; a plastic housing forming walls of liquid metal container;a rubber or plastic gasket or ring that forms a liquid tight seal tocontain the liquid metal; a metal plate forming bottom floor of liquidmetal chamber; a Peltier device(s) for heating and cooling; and a metalheat sink for removing heat from Peltier device(s).

FIG. 5 illustrates a view of a sandwich embodiment of a thermal cyclercomponent comprising a heat block comprising a liquid metal. (A) Thisview shows a liquid metal chamber is formed between two Peltier devices(two large walls) and the brown plastic piece, built as a square plasticring (four narrow walls). The liquid metal chamber comprises holes forcapillary samples tubes. Further, each Peltier device is thermallycoupled to a heat sink, which is in turn connected to a fan. (B) A closeup of the central portion of the heat block sandwiched between thePeltier devices. (C) the liquid metal chamber comprises holes forcapillary samples tubes. Capillary tubes are slid into holes, andimmersed directly in liquid metal composition for thermal cycling.Peltier devices are located on both sides of liquid metal reservoir toallow rapid heating and cooling.

FIG. 6 illustrates an embodiment for detecting a signal from a samplevessel cycled in a heat block comprising a liquid metal composition. AnLED is used to excite the sample contained within the sample vessel andany resulting signal is detected by a PIN photodiode.

FIG. 7 illustrates PCR amplification using primers specific for the HBVvirus and a patients blood sample, wherein the PCR was run on a RocheLightcycler. The melting curve's positive peak (green) indicates an HBV+test, but the negative control peak (brown) is also prominent.

FIG. 8 illustrates PCR amplification using the same primers and sampleas that used in FIG. 7, wherein the PCR was carried out using a thermalcycler comprising a liquid metal heat block. The positive peak (green)indicates an HBV+ test, and the negative control peaks (brown, pink) aremuch less prominent than in FIG. 7. This is indicative of a moreaccurate HBV+ test result.

FIG. 9 illustrates results from PCR performed in a thermal cyclercomprising a liquid metal heat block in comparison with results from aRoche Lightcycler. Melting curves were run simultaneously with twosamples: one in which PCR was performed In a Roche Lightcycler (green)and one in which PCR was performed in our invention (brown). The RochePCR produced an extra peak, at a temperature indicative of primer-dimerformation, indicating PCR performed in the Roche machine was lessaccurate than PCR performed in a thermal cycler comprising a liquidmetal heat block.

FIG. 10 illustrates an embodiment of the liquid composition heat blockthat uses resistive heating wires to heat the liquid composition. Thetop view shows wire arranged to provide uniform heating, wherein thewire are placed at a higher density near the edge of the liquidcomposition chamber and at a lower density near the center. Thisarrangement compensates for any possible edge effects which occur inconventional thermal cycler designs due to heat loss. As shown in theside view, the wires are suspended in the liquid composition, instead ofresting on the bottom, such that liquid metal contacts the wires on allsides; this allows for maximum heat transfer uniformity.

FIG. 11 illustrates the use of a liquid composition heat block for acontinuous PCR device. Multiple samples are continuously run throughsaid device to detect one or more specific biological specimens, such asa pathogen or biological contaminant.

FIG. 12 illustrates melting curves from samples in which PCRamplification was performed inside a stainless steel sample vessel incomparison to a conventional glass capillary tube. The melt curve isnearly the same for both reactions, indicating a successfulamplification. (A) Results from a PCR reaction performed in aconventional thermal cycler using metal sample vessels. PCR was carriedout for 40 cycles then SYBR green was used to detect the production of aPCR amplicon. (B) Results from a PCR reaction performed in aconventional thermal cycler using commercially available sample vessels.PCR was carried out for 40 cycles then SYBR green was used to detect theproduction of a PCR amplicon.

FIG. 13 illustrates a method of manufacture for metal sample vessels.This method can rapidly and inexpensively produce sample vessels bycutting and crimping them from a pulled metal stock in one movement. Thegroove is used to prevent the sample vessel walls from flaring out.

DETAILED DESCRIPTION OF THE INVENTION

This invention provides an apparatus comprising a thermal cycler forcycling the temperature of a sample vessel containing a reactionmixture, an optical assembly for detecting signal from the sample vesseland control means for controlling the operation of the thermal cyclerand the optical assembly. In certain embodiments the thermal cycleremploys a heat block comprising a liquid composition (such as a liquidmetal or a thermally conductive fluid) with high thermal conductivity torapidly cycle the temperatures in the sample vessel. The use of a liquidmetal provides two main advantages. First, metal has high thermalconductivity, providing rapid heat transfer. Second, liquid providestighter contact between the thermally conductive material and the samplevessel, providing more uniform heat transfer. As a result, thetemperatures within the sample vessels are remarkably uniform. Thecombination of rapid temperature ramp rates and uniformity oftemperature decreases nonspecific hybridization and significantlyincreases the specificity (e.g., signal-to-noise ratio) of amplificationin PCR within individual sample vessels as well as across multiplesample vessels located in the same heat block. In another embodiment,the sample vessel, alone or in combination with the thermal cycler,emits substantially all of a signal generated therein out through adiscrete portion of the sample vessel, for example, the top of thevessel, whereby the emitted light can be collected by the opticalassembly. In yet another embodiment a light detector detectssubstantially all of the light emitted from a sample vessel. In certainembodiments the liquid metal or sample vessel is highly reflective andreflects light transmitted through the walls of a transparent samplevessel back into the sample vessel. In this way, a greater proportion ofa light signal generated inside the sample vessel is emitted from adiscrete portion of the sample vessel, whereby it can be collected bythe optical assembly. The ability to collect more light from thereaction means that less expensive optics can be employed in the device,thereby decreasing the cost. Furthermore, collecting light from adiscrete location of the vessel eliminates the necessity of removing thevessel from the heat block when performing real time PCR. Thus, theconfiguration of the heat block allows rapid ramp times and uniformtemperatures, and the collection of reflected light from the top of thevessel by the optical assembly without removing the vessels from theheat block, allows real time PCR to proceed more quickly. Accordingly,the apparatus of this invention is particularly adapted for performingPCR (polymerase chain reaction), reverse transcription PCR and real timePCR. Thermal cyclers comprising the liquid metal heat block will performPCR faster and more cheaply than devices presently available on themarket. In one embodiment a thermal cycler comprising a heat blockcomprising a liquid composition is powered by a battery. In anotherembodiment a thermal cycler comprising a heat block comprising a liquidcomposition is powered by a AC or DC current.

In addition to heating blocks for PCR, the liquid metal heating blocksof the present invention can be used widely in the field ofbiotechnology and chemistry. Examples include but are not limited toincubations of enzymatic reactions such as restriction enzymes,biochemical assays and polymerase reactions; cell culturing andtransformation; hybridization; and any treatment requiring precisetemperature control. Based on the present disclosure, one of ordinaryskill in the art can readily adapt the liquid metal technology tovarious analyses of biological/chemical samples which require accuratetemperature control.

Thermal Cycler

The use of a liquid composition, such as a liquid metal or a thermallyconductive fluid, as a heating and cooling medium for a heating block,results in a more uniform heat transfer and more rapid heating andcooling cycles than solid metal heat blocks. In embodiments where aliquid metal heat block is used as a thermal cycler, the faster heatramping, and superior thermal uniformity lead to lower error rates byDNA polymerases than when used in conventional thermal cyclers (FIGS.7-9). This is due to the decreased time in which the PEAR sample spendsat sub-optimal temperatures. Further, the error rates are decreasedduring long amplifications, SNP identification and sequencing reactions,because of the enhanced thermal uniformity.

In one embodiment a liquid metal or a thermally conductive fluid is usedas a heating and cooling medium for a heating block, wherein the heatblock comprises at least a base and walls to contain the liquid metal ora thermally conductive fluid. The liquid metal or a thermally conductivefluid provides a more uniform temperature throughout the heat block thanconventional heat blocks, because of faster heat transfer within theliquid metal or a thermally conductive fluid and the ability to useconvection or stirring to distribute heat.

In another embodiment the heat block comprises a liquid metal orthermally conductive fluid in direct contact with sample vessels. Inthis embodiment full contact with sample vessels can be achieved,resulting in uniform heat transfer regardless of the type, size, andshape of the sample vessels. Pre-formed wells are not required.Furthermore, uniformity of temperature within the heating block can beachieved, because the liquid metal or thermally conductive fluid caneasily be circulated in the heating block by convection or by anexternal force, including but not limited to a stir bar, a pump, avibration device, or magnetohydrodynamic (MHD) force.

In yet another embodiment the liquid metal or thermally conductive fluidis completely contained within the heat block and does not contact thesample vessels. In this embodiment the container has receptacles whichare designed to accept sample vessels of a desired shape and size. Thesereceptacles are designed to closely fit the sample vessels placed in thewells. In one embodiment these receptacles are made out of asubstantially transparent material that allows light transmitted intothem to be reflected back into the sample vessel from the liquid metal.In an alternative embodiment the receptacles are made out of areflective material that reflects substantially all of the light toenter or that is created in a sample vessel in a receptacle well backinto said sample vessel. In another embodiment the receptacle may bemade out of an opaque material that is neither transparent norsubstantially reflective.

In one embodiment the receptacle is manufactured from a flexiblematerial, so that the wells of the receptacle conform to fit tightlywith the sample vessels. The tightness of the contact between the wellsof the receptacle and the sample vessels increases as the heat blockincreases in temperature and the liquid metal or thermally conductivefluid expands in volume. The receptacles may be manufactured from anopaque, transparent, semi-transparent or translucent material.

In either the open or closed embodiment the heat block may optionallyinclude a reservoir of liquid metal or thermally conductive fluid whichmay be part of the heat block, such as depression or bulge in bottom orsidewall of the heat block, or as a separate reservoir connected to theheat block by a connector, such as a tube. This reservoir can optionallybe connected by a pump to the heat block. Depending on its design thereservoir can serve as an overflow to capture any liquid metal orthermally conductive fluid as it expands beyond the volumetric limits ofthe heat block, to maintain or alter internal pressure in a sealed orclosed heat block, or as a reservoir for liquid metal lost during use.

In one embodiment the reservoir is used to replenish the liquid metal ora thermally conductive fluid during operation of the heat block. Areservoir containing additional liquid metal or a thermally conductivefluid may be provided to replenish losses as they occur. Thereplenishment system may keep the liquid metal at a desired level, or inclosed embodiments keep the liquid metal or a thermally conductive fluidat a desired pressure. In one embodiment a detection system is providedthat electrically monitors the level of liquid metal or a thermallyconductive fluid and warns the operator when it is low. Thisreplenishment system may take any convenient form such as a side orbottom secondary reservoir fitted with a plunger or pump to displaceliquid metal or a thermally conductive fluid, a control to operate theplunger or pump, and a sensor. For example the sensor may comprise awire positioned at a defined height which completes a circuit with theliquid metal when the liquid metal is at a desired height. In anotherembodiment the sensor may comprise an optical beam such that the opticalbeam shines horizontally at the top of the cavity containing the liquidmetal and illuminates the sensor if the liquid level is too low. Inanother embodiment the sensor comprises two optical beams, one above theother, the lower one indicating a low level and the upper one a highlevel. A signal can be relayed to the operator or to a control devicethat would indicate the level of the liquid metal or a thermallyconductive fluid. The signal can either indicate to an operator thatcorrective action should be taken (by raising or lowering the level ofliquid metal or a thermally conductive fluid). In another embodiment thecontrol system automatically adjusts the level of the liquid metal or athermally conductive fluid to reach a desired level. In yet anotherembodiment the liquid metal or a thermally conductive fluid heat blockcomprises a user accessible chamber that the user can replenish withliquid metal or a thermally conductive fluid as needed. In oneembodiment, the user accessible chamber connects with the liquid metalor a thermally conductive fluid heat block chamber at the bottom and canbe filled from the top.

Swap Block

In one embodiment, a thermal cycler body (101; 151) comprises a fan(103; 153) and a removable heat block assembly, or swap block (105; 155)(FIG. 1). The swap block (105; 155) is inserted into and removed fromthe thermal cycler body (103; 153) by optionally sliding the swap heatblock on sliding rails (113;163). After the swap block (105; 155) isinserted into the thermal cycler body (103; 153) the door of the thermalcycler (115;165) may be closed. The swap heat block (105; 155) comprisesa liquid composition container (111; 161) and a heat sink (107;157) andoptionally capped samples (109;159). In one embodiment the swap heatblock (FIG. 2) comprises a receptacle with wells that seals the in theliquid composition so that the sample vessels do not contact the liquid(metal, metal alloy or metal slurry). In another embodiment the swapblock (105; 155) comprises a receptacle barrier with wells (307;407)that is sealed to a liquid composition container housing (311;411),wherein the seal is liquid tight and may optionally comprise a gasket(309;409) (FIGS. 3 and 4). Further, the liquid composition containerhousing (311;411) is sealed to a base plate (313;413), which may be ametal plate (such as copper or aluminum), wherein the seal is liquidtight and may optionally comprise a gasket (312;412). The base plate(313;413) is in turn thermally coupled to a Peltier element (315;415),heats and cools the liquid composition and is in turn coupled to a heatsink (417). Optionally, a heat spreader (such as a copper, aluminum, orother metal or metal alloy that has high thermal conductivity) issandwiched between the base plate (313;413) and the Peltier element(315;415). In some embodiments the swap block (105; 155) is heldtogether by fasteners, such as screws (301;401). In one embodiment theswap block comprises a first piece, such as a receptacle with 48 wells(307;407), that is occupied by a second piece, such as a sample vessel,including but not limited to a sample plate (305;405), a single samplevessel or a strip of sample vessels, into which a third piece, such as atransparent cap plate (303;403), a single cap or strip of caps isinserted. In one embodiment the a transparent cap plate (303;403), asingle cap or strip of caps optionally comprises an extrusion, such as alight guide.

In another embodiment, the sample vessels are placed directly into theliquid. In yet another embodiment, the receptacles provide a ring (e.g.,O ring) that functions as a squeegee to wipe clean a sample vessel beingremoved from the liquid and optionally closes to seal the liquid metalin. In another embodiment, the receptacle provides a sleeve into whichthe sample vessel is placed (e.g., sleeve composed of a pliable plasticfilm); in other words, the sleeve functions as a barrier between thesample vessel and the liquid metal or thermally conductive fluid.

Liquid composition (such as liquid metal or thermally conductive fluids)heating blocks maintain a uniform temperature throughout the block. Inone embodiment this is achieved through passive forces such asconvection currents or passive conduction in a liquid metal or thermallyconductive fluid. In an alternative embodiment temperature uniformity isenhanced by actively mixing the liquid metal or thermally conductivefluid using a method such as a stir bar, or a circulation system using apump or an MHD force.

In one embodiment a pump is used to circulate the liquid metal orthermally conductive fluid in the heat block. Any pump design which candisplace the liquid metal or thermally conductive fluid is suitable,such as a positive displacement pump (including but not limited to arotary-type pump, reciprocating-type pump, roots type pump, a syringepump, a Wendelkolben pump or a helical twisted roots pump) a centrifugalpump, an MHD pump, or a kinetic pump. In this embodiment the pump willbe manufactured out of materials capable of withstanding the temperaturedifferentials and/or corrosive issues associated with liquid metal orthermally conductive fluids.

In another embodiment, a pump is utilized to circulate the liquid and/orto cause the liquid metal or thermally conductive fluid (e.g., increasedpressure in the reservoir chamber) to press against the receptacle wallsor sample walls depending on the configuration of the thermal cycler(e.g., open versus closed). For example, in a closed system, theincreased pressure causes the liquid to exert pressure against thereceptacle walls, thus causing such walls to press closely against thesample vessel walls, forming a junction. Such junction enhances thermalconductivity and/or optical transmittance. In embodiments where an opensystem is used (e.g., the sample vessels are in direct contact with aliquid composition) the pump may increase the level of the liquid metalor thermally conductive fluid such that it contacts a greater surfaceareas of the receptacle walls.

In another aspect of the invention, where samples are placed directlyinto the liquid (metal, metal alloy or metal slurry), such samplevessels would naturally be subject to buoyant force equal to thedisplacement of liquid. In various embodiments, a clip, lid, fastener,weight, spring clasp, screw plate, or such means is utilized to ensurethe sample vessels are firmly kept in place.

In an alternative embodiment a MHD force is used to circulate the liquidmetal. The liquid metal is exposed to a magnetic field formed in onedirection and an electrical field formed in a direction perpendicular tothe direction of the magnetic field. The liquid metal then flows in adirection perpendicular to both the direction of the magnetic field andthe direction of the electrical field. By using both a magnetic fieldand an electrical field, it is possible to cause liquid metal to flow ina designated direction without physical control such as control by apump. These field characteristics can be used to introduce currents inthe heat block in order to maintain a uniform temperature or tointroduce and discharge liquid metal into and from the heating block,for example to a reservoir. In a related embodiment the electrical fieldis formed by DC or AC current, as the frequency is modulated, the flowof the liquid metal oscillates in relation to the change in frequency,thereby achieving high uniformity of temperature throughout the heatblock.

In another embodiment the liquid metal or thermally conductive fluid maybe circulated by a stir bar. The stir bar may be linked to a motor whichcauses it to stir, or it may be magnetically responsive and stir inresponse to a change in magnetic field. In one embodiment the stir baris resistant to rapid changes in temperature or it is coated with acovering that is resistant to rapid changes in temperature. In oneembodiment the stir bar is a simple horizontal bar. In an alternativeembodiment the stir bar may be fan shaped or have multiple projections(such as 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12) which serve to stir theliquid metal or thermally conductive fluid. In one embodiment thethermal cycler (101) comprises a motor operatively linked to a fan (103)and a stir bar. In another embodiment the fan and stir bar are connectedcoaxially to the same motor and optionally turn simultaneously.

In yet another embodiment the liquid metal or thermally conductive fluidmay be circulated by a vibration device. The vibration device may beintegrated into the thermal cycler or heat block structure, or it may bea secondary device in contact with the heat block or thermal cycler. Thevibration device will transfer waves of vibration through the liquidmetal or thermally conductive fluid, aiding in its convection anddecreasing the time it takes for the metal to reach thermal uniformity.In one embodiment an acoustical device is used to vibrate the liquidmetal or thermally conductive fluid, such as a piezo mixer, ultrasonicvibrator, subsonic vibrator or other sonic device. The vibrator maycomprise speaker coils or piezos or mechanical motors. Vibratory devicesalso may shake the sample and PCR reagents in the sample vessels thusmixing the contents allowing the reaction to occur more efficiently

Liquid metals or a thermally conductive fluid are flowable during theoperation of a thermal cycler and have a boiling point higher than theoperation temperature. Further, the liquid metal or thermally conductivefluid is preferably non-toxic under conditions of operation. Liquidmetal has high heat and electrical conductivity and thus can be veryresponsive to heating and cooling patterns/cycles. For polymerase chainreaction (PCR), rapid heating and cooling rates are preferred, whichliquid metals or thermally conductive fluids can satisfy.

Sandwich Heat Block

In another aspect of the invention, the thermal cycler comprises asandwich liquid composition heat block (FIG. 5). In an embodiment thesandwich heat block comprises a liquid composition container(501;551;571) that is thermally coupled to Peltier heating and coolingelements (503;553;573), which is in turn thermally coupled to heat sinks(505;555;575) and optionally coupled to flanking fans (507;557). In thisembodiment the liquid composition container (501;551;571) comprisesopenings for sample vessels (559;579) such as capillary tubes (581). Inone embodiment the sample vessels are indirect contact with the liquidcomposition. In an alternative embodiment, the samples are physicallyseparated from the liquid composition by thermally conductive deformabletube. In one embodiment the heat sink comprises tubes or fins forincreasing the radiative surface of the heat sink. In another embodimentthe openings for the sample vessels (559;579) comprise a rubber orplastic O-ring which acts to form a seal around the sample vessel placedthrough the opening into the liquid composition and to squeegee off theliquid composition that may adhere to the sample vessel upon itswithdrawal from the heat block. Sandwich heat block embodiments maycomprise openings for at least 1 sample vessel, such as 2, 3, 4, 5, 6,7, 8, 10, 12, 16, 20, 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90,96, 192, or 384 sample vessels.

In another embodiment, holes are provided on both sides so that the topsand bottom of the sample vessels are visible. In such an embodiment, theliquid is encased in the plastic barrier with holes going through theplastic barrier (e.g., multiwell configuration) so that a sample vesselsits in a well. In this configuration a photodiode and optical detectormay be arrayed on opposite sides of a given well. This allows realtimeor quantitative PCR to be performed by inducing a light signal into onepart of the sample vessel (e.g. the top) and detecting any emanatingsignal from the other side of the block (e.g. the bottom), or viceversa.

In one embodiment, one or more capillary tubes (581) of a thermallyconductive plastic, such as that available from Cool Polymers (Inc., 333Strawberry Field Rd., Warwick, R.I. 02886 USA;http://www.coolpolymers.com) is inserted into a heat block comprising aliquid metal (501;551;571). In one embodiment the capillary tube (581)may penetrate through the opposing side of said heat block, providingoptical access to both the top and bottom of the tube. In thisembodiment a sample within the tube (581) can be excited on one end andany resulting signal can be detected on the other. In one embodiment thetube (581) directly contacts the liquid metal. In an alternativeembodiment the tube (581) is inserted into a highly thermally conductivedeformable tube (such as a plastic tube) within the liquid metalcomprised within the heat block. In this embodiment it is possible toinsert a sample vessel into the highly thermally conductive deformableplastic tube. The liquid metal could then be pressurized by using apump, wherein the pressure squeezes the thermally conductive plastictube to form a tight contact with the sample vessel.

Continuous Flow Heat Block

In an alternative embodiment the liquid metal or thermally conductivefluid heat block may be used in a continuous PCR thermal cycler.Continuous PCR thermal cyclers can be used when highly sensitive or highthroughput PCR is desired. There are many situations in which one mightwant to sample air, blood, water, or other medium continuously in asensitive PCR assay. This can be used to look for a variety ofbiological contaminants including influenza, bacterial pathogens, andany number of viral or bacterial pathogens. Continuous PCR allows PCR tobe practiced in an automated manner without the need for humaninteraction. A continuously sampling PCR system can also serve as anearly warning system in HVAC systems of buildings, airplanes, busses,and other vehicles, and can be used in the monitoring of blood, water,and other possibly contaminated sources.

In one embodiment the continuous PCR system takes an sample from acollection device, such as all air sampler, fluid sampler or othersampler, (1101) (FIG. 11). In other embodiments condensate fluidcollected on the condenser unit of an air conditioning system is used asa starting sample or a specialized gas sampling device that worksthrough direct impaction is used to obtain a sample. The sample isprepared (1103), which in some embodiments may include cell lysis, DNAor RNA purification, filtration, and/or reverse transcription. Then thesample is prepared for PCR (1105) by adding the sample to PCR reagents(such as at least one DNA polymerase, dNTPs, buffer and a salt) andprimers, (such as assay-specific primers or broadly applicable primersets for multiple target pathogens). These primers may be chosen toselectively amplify the DNA or cDNA isolated from a specific pathogen(such as a mold, virus, bacteria, parasite or amoeba), gene, otherdesired nucleic acid, or any combination thereof.

The PCR sample/reagent cocktail (1107) then flows through a tube to thethermal cycling unit (1109). In some embodiments the tube is a clear ortransparent. In another embodiment the tube is opaque. In one embodimentthe tube is a cylinder. In another embodiment the tubes cross sectioncomprises one or more planes forming a shape such as a triangle, square,rectangle, pentagon, hexagon, heptagon, octagon, nonagon, decagon, orother polygon. In one embodiment the volume of sample (1107) is suchthat it takes up a small discrete length of space in the sample vessel,the rest of which is occupied by air, gas, or non-reactive liquid, suchas mineral oil. Compressed gas or liquid is used to push the sample intothe heat block of the thermal cycler. In one embodiment the heat blockis a liquid metal or thermally conductive fluid heat block, which may beheated and cooled by a variety of devices, including but not limited tothermo-coupled Peltier thermoelectric module, a conventionalthermoelectric module, hot air or hot light. In one embodiment thethermal cycler uses Peltier thermoelectric modules external to the tubeto heat and cool the sample as desired.

After the desired number of thermal cycles are complete, the sample ispushed further down the tube using compressed air or liquid, exiting thethermal cycling region and passing into a detection region (1113) inwhich a fluorescence measurement, absorbance measurement, or otherinterrogation measurement can be made. In one embodiment the tube isopaque except for the detection region, which is clear or substantiallytransparent. In the detection region, a light source such as a coherentlight source including but not Limited to a laser) is used to excitefluorescent dyes (such as intercalating dyes, including but not limitedto ethidium bromide or SYBR green and related dyes) in the PCR sample,and the excitation light is sensed with a photodetector (such as a CCD,CMOS, or other optical detector). The detection electronics (1115)evaluate the signal sent from the detection region (1113) A positive PCRtest will yield larger amounts of detected fluorescence than will anegative PCR test.

Next the sample is pushed further down the tube, eventually to becollected as waste in the waste collector (1117). In one embodiment thetube is used for a single use only, then disposed of. In an alternativeembodiment the tube can be used to amplify and detect the presence orabsence of amplification products in multiple samples. The samples areloaded at intervals and interspaced with a barrier of gas or liquid toprevent intermixing. The samples are spaced apart in the transport tube,allowing each one to be individually cycled and detected. In oneembodiment the samples are spaced apart in a manner so that as one isundergoing thermal cycling another sample is in the detection regionundergoing interrogation. In another embodiment multiple tubes may beused in parallel to increase sample throughput. In yet anotherembodiment the system may alert the user when amplification has occurred(a positive result), indicating that the target sequence is present.

Gradient Heat Block

In an alternative embodiment the liquid metal or thermally conductivefluid heat block is designed so that it can maintain differenttemperatures in different zones of the heat block. This allows differentsample vessels located in wells in different zones to be cycled atdifferent temperatures simultaneously, such as during gradient PCR. Inone embodiment the liquid metal or thermally conductive fluid heat blockis a capable of maintaining a temperature gradient across 2 or morezones, such as 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, or 24 zones. In an embodiment the heat blockcomprises a receptacle with 1 or more sample vessel wells in eachtemperature zone, such as 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 wells. In one embodimenttemperature gradients in excess of 0.1° C. to 20° C. across the liquidmetal or thermally conductive fluid heat block can be achieved.

In one embodiment the temperature gradient changes in a linear fashionacross a single dimension (horizontally or vertically) of the liquidmetal or thermally conductive fluid heat block. For example in a heatblock comprising a receptacle with 48 wells (307;407) there are 8 rowsof 6 wells equally spaced across the block. If a temperature gradient of8° C. is formed horizontally across the top of the heat block, each rowof sample wells will differ in temperature by approximately 1° C.

In some embodiments the heat block will contain internal baffles orinsulated walls which act to separate different zones of the liquidmetal or thermally conductive fluid from other zones. Each zone mayfurther comprise an individual heat mixer (such as a pump, stir bar orMHD) or the entire heat block may be attached to a single heat mixersuch as a MHD or vibration device. Further each zone of the heat blockmay comprise individual heating and/or cooling elements such as a heatconduction element (wires, tubes), thin foil type heater, Peltierelements or cooling units.

In an alternative embodiment the heat block may comprise multipleheating and cooling devices, some of which act globally across all ofthe liquid metal or thermally conductive fluid heat zones, and some ofwhich act only within a single zone. For example the heat block mayemploy uniform heating across the entire length and width of block withadditional heating and/or cooling devices adjacent to each zone in theheat block Such an arrangement may provide greater precision forprecisely tuning the temperature of the liquid metal or thermallyconductive fluid in each zone and the reaction temperature of theassociated sample vessels within said zone.

Thermal Conductivity

The liquid composition heat block, containing a liquid metal orthermally conductive fluid, maintains a more uniform temperature acrossthe block in comparison to solid metal heat blocks. Solid heating blocksshow a significant variation in temperature both across the block and insample to sample variation (Schoder et al., J. Clin. Micro Biol. 2005,43 2724-2728). The variability of temperature at any given point in theheating apparatus is greater for the conventional solid metal thermalcycler than for the liquid metal or thermally conductive fluid heatblock. Variability as high as +/−3.3° C. has been observed withconventional thermal cyclers while the greatest variability with theliquid metal or thermally conductive fluid heat block is much lower. Inone embodiment the heat block comprises a liquid metal with a heattransfer coefficient greater than 0.1 watts/meter-Kelvin (W/m*K), suchas between 0.25-85 W/m*K, including but not limited to 0.25 W/m*K, 0.5W/m*K, 0.75 W/m*K, 1 W/m*K, 1.5 W/m*K, 2 W/m*K, 2.5 W/m*K., 3 W/m*K, 3.5W/m*K, 4 W/m*K, 4.5 W/m*K, 5 W/m*K, 5.5 W/m*K, 6 W/m*K, 6.5 W/m*K, 7W/m*K, 7.5 W/m*K, 8 W/m*K, 8.5 W/m*K, 9 W/m*K, 9.5 W/m*K, 10 W/m*K, 11W/m*K, 12 W/m*K, 13 W/m*K, 14 W/m*K, 15 W/m*K, 16 W/m*K, 17 W/m*K, 18W/m*K, 19 W/m*K, 20 W/m*K, 21 W/m*K, 22 W/m*K, 23 W/m*K, 24 W/m*K, 25W/m*K, 26 W/m*K, 27 W/m*K, 28 W/m*K, 29 W/m*K, 30 W/m*K, 32 W/m*K, 35W/m*K, 37 W/m*K, 40 W/m*K, 42 W/m*K, 45 W/m*K, 47 W/m*K, 50 W/m*K, 55W/m*K, 60 W/m*K, 65 W/m*K, 70 W/m*K, 75 W/m*K, 80 W/m*K, 85 W/m*K.

In one embodiment the liquid metal or thermally conductive fluid heatblock is a component of a thermal cycler which has substantial thermaluniformity across the entire heat block, wherein the temperature betweenany two sample vessels in the heat block has a variance of no more than+/−0.6° C., such as no more than +/−0.59° C., +/−, 0.58° C., +/−0.57°C., +/−0.56° C., +/−0.55° C., +/−0.54° C., +/−0.53° C., +/−0.52° C.,+/−0.51° C., +/−0.5° C., +/−0.49° C., +/−, 0.48° C., +/−0.47° C.,+/−0.46° C., +/−0.45° C., +/−0.44° C., +/−0.43° C., +/−0.42° C.,+/−0.41° C., +/−0.4° C., +/−0.39° C., +/−0.38° C., +/−0.37° C., +/−0.36°C., +/−0.35° C., +/−0.34° C., +/−0.32° C., +/−0.31° C., +/−0.3° C.,+/−0.29° C., +/−0.28° C., +/−0.27° C., +/−0.26° C., +/−0.25° C.,+/−0.24° C., +/−0.23° C., +/−0.22° C., +/−0.21° C., +/−0.2° C., +/−0.19°C., +/−0.18° C., +/−0.17° C., +/−0.16° C., +/−0.15° C., 0.14° C.,+/−0.13° C., +/−0.12° C., +/−0.11° C., +/−0.1° C., +/−0.09° C., +/−0.08°C., +/−0.07° C., +/−0.06° C., +/−0.05° C., +/−0.04° C., +/−0.03° C.,+/−0.02° C., +/−0.01° C., +/−0.009° C., +/−0.008° C., +/−0.007° C.,+/−0.006° C., +/−0.005° C., +/−0.004° C., +/−0.003° C., +/−0.002° C., or+/−0.001° C. In another embodiment the liquid metal or thermallyconductive fluid heat block has a substantially uniform temperaturebetween any two wells in the heat block receptacle with a variance froma desired temperature of no more than +/−0.6° C., such as no more than+/−0.59° C., +/−0.58° C., +/−0.57° C., +/−0.56° C., +/−0.55° C.,+/−0.54° C., +/−0.53° C., +/−0.52° C., +/−0.51° C., +/−0.5° C., +/−0.49°C., +/−0.48° C., +/−0.47° C., +/−0.46° C., +/−0.45° C., +/−0.44° C.,+/−0.43° C., +/−0.42° C., +/−0.41° C., +/−0.4° C., +/−0.39° C., +/−0.38°C., +/−0.37° C., +/−0.36° C., +/−0.35° C., +/−0.34° C., +/−0.32° C.,+/−0.31° C., +/−0.3° C., +/−0.29° C., +/−0.28° C., +/−0.27° C., +/−0.26°C., +/−0.25° C., +/−0.24° C., +/−0.23° C., +/−0.22° C., +/−0.21° C.,+/−0.2° C., +/−0.19° C., +/−0.18° C., +/−0.17° C., +/−0.16° C., +/−0.15°C., 0.14° C., +/−0.13° C., +/−0.12° C., +/−0.11° C., +/−0.1° C.,+/−0.09° C., +/−0.08° C., +/−0.07° C., +/−0.06° C., +/−0.05° C.,+/−0.04° C., +/−0.03° C., +/−0.02° C., +/−0.01° C., +/−0.009° C.,+/−0.008° C., +/−0.007° C., +/−0.006° C., +/−0.005° C., +/−0.004° C.,+/−0.003° C., +/−0.002° C., or +/−0.001° C. In yet another embodiment asample vessel in the liquid metal or thermally conductive fluid heatblock has a uniform temperature within the sample vessel with a variancefrom a desired temperature of no more than +/−0.6° C., such as no morethan +/−0.59° C., +/−0.58° C., +/−0.57° C., +/−0.56° C., +/−0.55° C.,+/−0.54° C., +/−0.53° C., +/−0.52° C., +/−0.51° C., +/−0.5° C., +/−0.49°C., +/−0.48° C., +/−0.47° C., +/−0.46° C., +/−0.45° C., +/−0.44° C.,+/−0.43° C., +/−0.42° C., +/−0.41° C., +/−0.4° C., +/−0.39° C., +/−0.38°C., +/−0.37° C., +/−0.36° C., +/−0.35° C., +/−0.34° C., +/−0.32° C.,+/−0.31° C., +/−0.3° C., +/−0.29° C., +/−0.28° C., +/−0.27° C., +/−0.26°C., +/−0.25° C., +/−0.24° C., +/−0.23° C., +/−0.22° C., +/−0.21° C.,+/−0.2° C., +/−0.19° C., +/−0.18° C., +/−0.17° C., +/−0.16° C., +/−0.15°C., 0.14° C., +/−0.13° C., +/−0.12° C., +/−0.11° C., +/−0.1° C.,+/−0.09° C., +/−0.08° C., +/−0.07° C., +/−0.06° C., +/−0.05° C.,+/−0.04° C., +/−0.03° C., +/−0.02° C., +/−0.01° C., +/−0.009° C.,+/−0.008° C., +/−0.007° C., +/−0.006° C., +/−0.005° C., +/−0.004° C.,+/−0.003° C., +/−0.002° C., or +/−0.001° C.

In some embodiments the uniformity of temperature of the liquid metal orthermally conductive fluid heat block is regulated by circulating theliquid metal or thermally conductive fluid in the block. Circulation ofthe liquid metal or thermally conductive fluid can be created by naturalconvection or forced convection, such as by the intervention of a deviceincluding but not limited to a stir bar, a pump or MHD power, vibrationby physical force or MHD power with DC or AC current, etc.

In some embodiments the liquid metal or thermally conductive fluid heatblock has a ramp rate or can change temperature at a rate substantiallyfaster than conventional metal heat blocks, such as at a rate of atleast 5-50.5° C. per second, including but not limited to a range of atleast 10-40° C. per second, more specifically at a rate of at least 5°C., 5.5° C., 6° C., 6.5° C., 7° C., 7.5° C., 8° C., 8.5° C., 9° C., 9.5°C., 10° C., 10.5° C., 11° C., 11.5° C., 12° C., 12.5° C., 13° C., 13.5°C., 14° C., 14.5° C., 15° C., 15.5° C., 16° C., 16.5° C., 17° C., 17.5°C., 18° C., 18.5° C., 19° C., 19.5° C., 20° C., 20.5° C., 21° C., 21.5°C., 22° C., 22.5° C., 23° C., 23.5° C., 24° C., 24.5° C., 25° C., 25.5°C., 26° C., 26.5° C., 27° C., 27.5° C., 28° C., 28.5° C., 29° C., 29.5°C., 30° C., 30.5° C., 31° C., 31.5° C., 32° C., 32.5° C., 33° C., 33.5°C., 34° C., 34.5° C., 35° C., 35.5° C., 36° C., 36.5° C., 37° C., 37.5°C., 38° C., 38.5° C., 39° C., 39.5° C., 40° C., 40.5° C., 41° C., 41.5°C., 42° C., 43.5° C., 44° C., 44.5° C., 45° C., 45.5° C., 46° C., 46.5°C., 47° C., 47.5° C., 48° C., 48.5° C., 49° C., 49.5° C., 50° C., and50.5° C. per second. In a related embodiment said liquid metal orthermally conductive fluid heat block can change temperature at a ratesubstantially faster than conventional metal heat blocks whilemaintaining a uniform temperature across the heat block and/or within asample within said heat block. In one embodiment the liquid metal heatblock can increase temperature at a rate of at least 44° C. per second.In another embodiment the liquid metal heat block can decreasetemperature at a rate of at least 17° C. per second. In one embodimentthe temperature of the liquid metal or thermally conductive fluid ismeasured with glass bead thermistors (Betatherm). In another embodimentan infrared camera is used to measure the temperature of the liquidmetal or thermally conductive fluid, or the liquid tight receptacle thatcovers the top of the heat block, or the temperature of the samplevessels. In another embodiment the temperature of the liquid metal orthermally conductive fluid is measured with an external probe. In yetanother embodiment the temperature of the liquid metal or thermallyconductive fluid is measured with a glass bead thermocouple. In anotherembodiment the temperature of at least one sample vessel is measuredwith a probe.

In some embodiments where the liquid metal or thermally conductive fluidheat block is used in a thermal cycler a series of PCR cycles may beperformed faster than conventional solid block thermal cyclers. A singlesimple PCR cycle normally includes a denaturation step, a hybridizationstep and an extension step, each performed at a specific temperature. Insome embodiments a series of 30 PCR cycles (PCR run) may be completed in1 to 20 minutes, such as 1 min, 2 min, 3 min, 4 min, 5 min, 6 min, 7min, 8 min, 9 min, 10 min, 11 min, 12 min, 13 min, 14 min, 15 min, 16min, 17 min, 18 min, 19 min, 20 min. However, the length of time of aPCR run is dependent not only on the speed and temperature uniformity ofthe thermal cycler. It will be clear to a practitioner in the art thatthe length of time of the PCR run can be varied depending on thecharacteristic of the desired PCR product.

Compositions

Thermally conductive materials that are liquid at temperatures at whichPCR is performed allow one to dip a sample vessel of any shape into thetemperature control material and to maintain good thermal contact forheat transfer. Accordingly, the composition preferably is liquid atleast in the range between primer annealing and duplex dissociation.Primer annealing occurs typically at around 55° C. but can be as high asabout 70° C. or as low as about 45° C. Duplex dissociation occurstypically around 94° C. but can be lower depending on factors such asthe length and percentage of guanine-cytosine base pairings (SC content)in the amplicon. Accordingly, in one embodiment the liquid compositionhas a melting temperature (i.e., transition from solid to liquid at) nogreater than 70° C. In an alternative embodiment, the liquid compositionhas a melting temperature no greater than 60° C. In an alternativeembodiment, the liquid composition has a melting temperature no greaterthan 50° C. In yet another embodiment, the liquid composition has amelting temperature no greater 40° C.

A variety of liquid metal compositions may be used in the practice ofthe claimed invention. In one embodiment the liquid metal compositionmay be gallium or a composition containing gallium. Some compositionsmay also comprise indium, copper, rhodium, silver, stannous, bismuth,tin and/or zinc. In one embodiment the liquid metal is obtained fromCoollaboratory (Http://coolaboratory.com). In some embodiments theliquid metal may contain from 40-80% gallium and from 10-50% indium. Insome embodiments the liquid metal alloy may contain from 1-40% copper,rhodium, silver, stannous, bismuth, tin, zinc or combinations thereof.In some embodiments the liquid metal alloy may comprise about 60%gallium about 25.0% indium about 14.0% Sn/about 1.0% Zn; about 62%gallium/22% indium about 16.0% Sn; about 75% gallium/about 25% indium;about 95% gallium/about 5% indium; or 100% gallium. In a anotherembodiment the composition may contain 60-99% gallium in combinationwith indium, such as about 75% gallium and about 25% indium. An alloywith about 75% gallium and about 25% indium becomes a liquid at about15.7° C. and has a boiling point of about 2,000° C. Such an alloy is ina liquid state but never reaches temperatures high enough to causevaporization during PCR thermal cycling. Therefore even in embodimentswhere the liquid metal directly contacts the sample vessels toxicity dueto vaporization of the liquid metal is not a problem.

In another embodiment a toxic liquid metal may be used in the presentinvention, such as mercury, mercury alloys or Woods metal. Woods metalwhich comprises about 50% Bi, 25% Pb, 12.5% Sn, 12.5% Cd has a highworking temperature range (70-350° C. A heat block comprising a liquidmetal such as woods metal can be used to boil biological samples or inany other laboratory technique requiring a stable high temperature heatblock.

In various embodiments, the liquid composition is a liquid metal, liquidmetal alloy or metal containing slurry. The expansion coefficient of theliquid metal will vary according to the precise components of a liquidmetal, metal alloy or slurry that are contemplated for use in thermalcyclers of the invention. In various embodiments, a liquid metal, liquidmetal alloy or metal slurry it expands in volume during PCR by about0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4,1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8,2.9 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9 4.0, 4.1, 4.2, 4.3,4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.5, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7,5.8, 5.9, or 6.0%, as compared to before PCR initiation.

In one embodiment a liquid metal, liquid metal alloy or metal containingslurry is designed to expand a sufficient amount to compress thejunction between a container receptacle and a sample vessel, forming atight contact. This contact provides enhanced thermal conductivity, aswell as optical transmittance (e.g., reflectance of light back into thesample vessel). This tight contact increases the thermal conductivitybetween the liquid metal and the sample vessel by decreasing the airspace separating the receptacle from the sample vessel. As one example,gallium exhibits a fairly uniform expansion.

TABLE 1 Gallium expansion Starting Temperature End Temperature Volumeexpansion 25° C. 55° C. +1.08% 55° C. 72° C. +0.61% 72° C. 95° C. +0.83%25° C. 95° C. +2.54%

In another embodiment the heat block comprise a liquid composition whichis a thermally conductive fluid. A variety of thermally conductivefluids may be used in the claimed invention. The term thermallyconductive fluids includes waxes and oils which have a working range oftemperatures suitable for use in a thermal cycler. In other words thewaxes and oils should have a relatively low melting temperature, in therange of 30-55° C. and maintain their stability at temperatures in atleast in the range of 30-110° C. A variety of waxes and oils aresuitable for use as thermally conductive fluids, including compoundssuch as, but not limited to hydrocarbon and silicon compounds andmixtures thereof. Examples include: silicone oil, carboxy-modifiedsilicone oil, mineral oil, dibutyl phthalate, polydiethylsiloxanes,polydimethylsiloxanes, tetraalkoxysilanes, silahydrocarbons,polyalphaolefins, naphthenic oils, hydroisomerized oils, parafinic oil,parrafin wax, paraffin wax, paraffin wax mixed with boron nitride,tricosane paraffin wax, polyorganosiloxane polymers, polyolefin wax,polyethylene wax or polypropylene wax and mixtures thereof. Further, thethermally conductive fluid may comprise additives which act to modifyits stability, viscosity, expansion coefficient, opacity, and/orreflectivity. Such additives include but are not limited to plastics,minerals aqueous fluids, antifreezes or metals.

Reflectivity

In one embodiment a liquid metal or thermally conductive fluid is usedthat reflects substantially all of the light it receives. In anotherembodiment the liquid metal or thermally conductive fluid is a componentin a heat block of a thermal cycler connected to an optical assemblythat is capable of exciting florescent molecules in a sample vessel anddetecting the signal. The sample vessels may be directly immersed in theliquid metal or thermally conductive fluid of the heat block, or beseparated from the liquid metal or thermally conductive fluid by areceptacle that is thermally conductive. In embodiments comprising areceptacle, the receptacle may be manufactured with substantiallytransparent or reflective material. In these embodiments the liquidmetal or thermally conductive fluid or reflective sample vessel surfacereflects back substantially all of the light it receives which can thenbe detected by a light detection device, including but not limited toCCD devices, CMOS devices, LED devices, PN photodiodes, PIN photodiodes,or photovoltaic cells. Further, in embodiments where a transparentreceptacle is used a transparent sample vessel may be used that consistsof the same plastic as the receptacle, or is manufactured from atransparent material with a similar index of refraction as thereceptacle.

In one embodiment the level of liquid metal or thermally conductivefluid is higher than the level of the sample in the sample vessel. Inother words when viewed from the side, the volume of sample and PCRreaction cocktail in the sample vessel is below the level of the liquidmetal or thermally conductive fluid. The liquid metal or thermallyconductive fluid will then substantially reflect any light which entersor is created in the sample vessel. In one embodiment the liquid metalor thermally conductive fluid heat block is a component in a real timethermal cycler comprising an optical assembly comprising a multi-channeldetection apparatus, such as multiple PIN diodes. For example theapparatus may comprise multiple single channels dedicated detectinglight from individual wells in the receptacle. In this embodiment theliquid metal or thermally conductive fluid acts as an optical bufferwhich substantially prevents the light transmitted into or out of afirst sample vessel from being detected by a detection channelassociated with a second sample vessel.

Sample Vessels

The term “sample vessels” includes reaction vessels of a variety ofshapes and configurations. In an embodiment sample vessels can be usedto contain reaction mixtures, such as PCR reaction mixtures, reversetranscription reaction mixtures, real-time PCR reaction mixtures, or anyother reaction mixture which requires heating, cooling or a stableuniform temperature. In one embodiment the sample vessels are round ortubular shaped vessels. In an alternative embodiment the sample vesselsare oval vessels. In another embodiment the sample vessels arerectangular or square shaped vessels. Any of the preceding embodimentsmay further employ a tapered, rounded or flat bottom. In yet anotherembodiment the sample vessels are capillary tubes, such as clear glasscapillary tubes or coated capillary tubes, wherein the coating (e.g.metal) increases internal reflectivity. In an additional embodiment thesample vessels are slides, such as glass slides. In another embodimentthe sample vessels are sealed at the bottom. In one embodiment thesample vessels are coated, at least externally, with anti-adhesioncoatings such as teflon or silane so as to reduce the adherence of aliquid composition, such as a liquid metal or thermally conductivefluid. In another embodiment the sample vessels are coated, at leastinternally, with a material for preventing an amplicon from sticking tothe sample vessel walls, such as a fluorinated polymer or BSA.

In one embodiment the sample vessels are manufactured and used asindividual vessels. In another embodiment the sample vessels are linkedtogether in a horizontal series comprising a multiple of individualvessels, such as 2, 4, 6, 10, 12, 14 or 16 tubes. In yet anotherembodiment the sample vessels are linked together to form a sheet, plateor tray of vessels designed to fit into the top of the heating block ofa thermal cycler so as to occupy some or all available reaction wells.In one embodiment the trays or sheets may comprise at least 6, wells, 12wells, 24 wells, 36 wells, 48 wells, 54 wells, 60 wells, 66 wells, 72wells, 78 wells, 84 wells, 90 wells or 96 wells, 144 wells, 192 wells,384 wells, 768, or 1536 wells.

In one embodiment the sample vessels have caps attached to their openend by a linking element, such as a plastic strip which is optionallyhinged. In another embodiment the sample vessels lack an attached cap.In one embodiment the sample vessels are designed to hold a maximumsample volume, such as 10 ul, 20 ul, 30 ul, 40 ul, 50 ul, 60 ul, 70 ul,80 ul, 90 ul, 100 ul, 200 ul, 250 ul, 500 ul, 750 ul, 1000 ul, 1500 ul,2000 ul, 5 mL, or 10 mL.

In some embodiments real-time polymerase chain reactions (PCR) areperformed in sample vessels manufactured from materials chosen for theiroptical clarity and for their known non-interaction with the reactants,such as glass or plastic. In one embodiment the sample vessels aredesigned so that light can enter and leave through the top portion ofthe sample vessel, which may be covered a cap capable of transmittinglight. In another embodiment the sample vessels are designed so thatlight can enter and leave the sample vessel through the bottom of thesample vessel. In one embodiment the sample vessels are manufacturedfrom a transparent or translucent material capable of transmittinglight. In one embodiment the sample vessels are designed so that lightis directed to exit through a single surface, such as the top or bottom.

In other embodiments the sample vessels are manufactured from materialsthat are substantially internally reflective, such as reflectiveplastic, coated plastic (such as with metal or other reflectivesubstances), coated glass (such as with metal or other reflectivesubstances), doped glass (manufactured with the addition of moleculesthat increase the reflectivity of the glass), or metal, including butnot limited to stainless steel, chromium, or other substantiallynon-reactive metals. Metal has a high strength that allows for muchthinner sidewalls than glass or plastic. This decreases the thermalbarrier between the reactants and external hot/cold sources, allowingfor better thermal control, greater spatial temperature uniformity, andmore rapid temperature changes, all of which can produce faster, moreefficient polymerase chain reactions. In embodiments whereepifluorescence is used to monitor real-time fluorescence, the highreflectivity of the internal metallic surface aids in the collection offluorescent light. In one embodiment the interior of the metal samplevessels is polished or electro-polished.

In one embodiment the metal sample vessels are manufactured from alarger cylindrical or rectangular stock. First the stock is pulled tothe desired diameter. Alternatively the standard methods of syringeproduction may be used. A continuous tube (such as a rectangular orcylindrical tube) is generated, which must be both cut and sealed toproduce pieces of a desired length, such as about 1 cM, 2 cM, 3 cM, 4cM, 5 cM, 6 cM, 7 cM, 8 cm, 9 cM, 10 cM or any length in between. In oneembodiment the diameter of the sealed end does not exceed the diameterof the tube itself. In this embodiment the tube is next cut and sealed:The tube (1301) may be fed through a groove (1303) in a metallic block(1305) (FIG. 13). In one embodiment the groove width is very close tothe outer diameter size of the metal tube. As the tube (1301) exits themetal block (1305), a cutting blade (1307) is lowered with its edgeflush with the metal block, perpendicular to the groove. In oneembodiment the blade (1307) is shaped with a tapered edge (1309). Inanother embodiment the blade is shaped with an edge such that both cutsand crimps shut the end of the metal tube, and the groove walls preventthe seal from flaring, forcing its diameter to remain close to thediameter of the bulk tube. After crimping, the vessel may requirefurther sealing. In one embodiment this can be accomplished with a smallweld or braze or solder. In another embodiment cutting and crimping canbe avoided by using a metal plug. If necessary the final sealed end canbe ground to decrease its diameter and to remove rough edges.

In alternative embodiment, the metal sample vessel may be pulled to thedesired diameter and cut into desired lengths. One end of each piece isthen forced into a hemispherical cup having a similar diameter to thetube itself. This motion may round off and crimp closed the metal tube.In a related embodiment a pin is inserted through the open top of themetal tube to aid in crushing the seal end of the tube into thereceiving cup. The tube can be crimp sealed in order to create a vesselwith one closed end and one open end suitable for PCR.

Sample Vessel Caps

It is generally desirable to cover the top of the sample vessel toprevent evaporation during PCR thermal cycling. This can be accomplishedby layering the top of the sample vessel with a layer of a non-reactiveliquid, such as mineral oil, sealing the sample vessel (such as by heatsealing a capillary tube) or by closing the sample vessel with a cap.

In one embodiment a cap is used. The cap may be manufactured using anysuitable material (such as glass or plastic) that forms a seal with thesample vessel and acts as a vapor barrier. In one embodiment the cap isa plastic cap. This cap may be opaque, translucent or substantiallytransparent. In one embodiment the cap is optically transparent and issuitable for use with a thermal cycler comprising a liquid metal orthermally conductive fluid heat block, and an optical assembly. Inanother embodiment the cap is partially or completely coated with anopaque coating. In yet another embodiment the cap is partially orcompletely coated with a reflective coating, such as a mirror coating.

The extraction of light from a sample vessel or vessel containing amaterial which fluoresces when pumped with an excitation wavelength canbe difficult to accomplish especially when the heat block occludes thevessel. A sample vessel cap (303;403) which is made of a clear material,such as plastic or glass, and which optionally comprises a lightguidethat can be optically coupled (with lenses, filters, beam splitters;e.g. FIG. 3) to a light source (such as a light emitter) and a detector,wherein the presence of the lightguide increases the amount of lightdelivered to the detector. The light emitter may be a coherent sourcesuch as a laser or a non-coherent source such as an LED.

In addition, an advantage of one of the exemplary embodiments of theinvention is that light emitted from a label/dye in the sample vessel isreflected back into the sample vessel based on the reflective propertyof the liquid metal or thermally conductive fluid, liquid metal alloy ormetal slurry. In a further embodiment, the amount of reflection isfurther enhanced by forming a better contact between the sample vesseland receptacle well (e.g., using the volume expansion to form a tightjunction, or by using a pump to increase the pressure inside the liquidcontaining chamber, so that the liquid exerts additional pressure on thewalls of the receptacle wells to form a tight junction with the samplevessels).

In another embodiment, a similar effect for light reflection is effectedby utilizing the specialized sample vessels of the invention, where asample vessel is comprised of an opaque composition (e.g., stainlesssteel) or is coated (internally/externally) with a opaque film (e.g.,aluminum) that is reflective. In one embodiment the sample vessel ismirror coated. In embodiments wherein the sample vessel comprises metal,the metal may be polished or electro-polished to increases itsreflectivity.

In either case, in various embodiments, cap implements of the inventionare comprised of a material that is optically clear, characterized byhaving low or no autofluorescence and forms a good seal with the samplevessel. Furthermore, in some embodiments, the cap provides of anextrusion (e.g., lightguide) that protrudes a certain length into thesample vessel. Examples of material that can be utilized in composingthe cap include but are not limited to acrylics, polycarbonates,polystyrenes, styrene block copolymers (SBCs), styrene acrylonitrile(SAN), ABS, polysulfones, thermoplastic polyesters (such as PET),polypropylene, acrylic-styrene copolymers (SMMA), PVC, nylon, cellulosicresins, cyclic olefin copolymers (COCs), allyl diglycol carbonate (ADC),Cyclic Olefins (such as TOPAS, ZEONOR and ZEONEX) and mixtures thereof.

In various embodiments, the cap and/or extrusion can be of a geometricshape which includes but is not limited to a polygon, elliptical,circle, square, rectangle, triangle, or any shape that can be obtainedthrough injection molding (as known in the art). Furthermore, it will berecognized that the sample vessels, as well as the receptacle wells canalso be of any of the shapes desired. In one embodiment, the cap, samplevessel, and receptacles are of the same geometric shape. In a furtherembodiment, the geometric shape is rectangular. In one embodiment, thegeometric shape, is selected based on the material used in each of thecap, sample vessel and receptacle walls, so as to provide enhancedcontact between the sample wall and receptacle wall, and provide optimumlight transfer out of the sample vessel. In yet a further embodiment,the refractive index of the sample vessel wall and the receptacle wallis equal or nearly equal.

In one embodiment, the cap and cap extrusion are comprised of the samematerial. In one embodiment, the cap, cap extrusion, sample vessel andreceptacle is each comprised of the same material or a differentmaterial, which are disclosed herein.

In some embodiments, the cap extrusion protrudes to a level in thesample vessel that is above, at or below the level (e.g., line) at whichthe liquid metal or thermally conductive fluid, liquid metal alloy orliquid metal slurry (collectively “liquid”) is positioned. In oneembodiment the protrusion is below the level of the liquid ispositioned.

In one embodiment, the light will travel the extrusion into the samplevessel and the resulting signal emitted from a label/dye in the sampletravels back up the extrusion; this light is emitted from asubstantially discrete portion of the cap where it is detected by aphotodetector, such as a photodiode (e.g., FIG. 6).

In one embodiment the tip of the cap is below the surface level of theliquid metal or thermally conductive fluid. If viewed from the side itwould be apparent that the tip of the cap was located below the level ofthe liquid metal or thermally conductive fluid in which the samplevessel was located so that it collects substantially all of the light.This is the case for embodiments where the sample vessel is directlyimmersed in the liquid metal or thermally conductive fluid as well asembodiments wherein the sample vessel is placed inside a receptaclewell.

The cap shape and surface quality can be designed to maximize opticalcoupling from the cap into the liquid. In another embodiment the cap maybe illuminated with a fiber bundle, or by a free space solution. Thefree space system may includes coupling lenses, and/or a beamsplitter.The optical system may simultaneously excite the fluorescing liquid, anddetect fluorescence.

In one embodiment the plastic cap may be fabricated either through castplastic, or injection molding.

In one embodiment, the cap readily absorbs the heat emitted from thethermal cycler/liquid so that the cap is heated to a temperature thatreduces or eliminates condensation. Often, with PCR methods in the priorart, the upper area/cap of a sample vessel would be at a coolertemperature than the lower portions of the sample vessel, thus reactionliquid would condense onto the colder surface thereby causing changes inthe chemistry of the reaction (e.g., changes in concentrations leadingto inefficient reactions or faulty results). In another embodiment thesample vessel is designed so that the sample vessel extends far enoughbelow the surface level of the liquid so that the top entrance of thesample vessel is far enough from the surface of the sample/PCR cocktailthat condensation is prevented. In yet another embodiment a lid ordownward pressure on the cap forces the sample vessel into a tightercontact with the receptacle, which may retard evaporation.

Means for Heating and Cooling the Composition

The liquid metal or thermally conductive fluid heat block can be heatedand cooled by using a variety of techniques known to a practitioner inthe art. In one embodiment a heat block heating component is selectedfrom a Peltier device, a resistive heater, and a radiative heater. Inone embodiment, a heat block cooling component is selected from aPeltier device, a heatsink, a refrigerator, an evaporative cooler, aheat pipe, a heat pump, and a phase change material. In one embodimentthe heating element may provided by extending a tube into the heatblock. The tube can be fitted with through which hot or cold fluids canbe pumped. In some alternative embodiments the liquid metal or thermallyconductive fluid heat block can be fitted with a heating and/or coolingcoil, or with an electrical resistance heater arranged to prevent edgeeffects. In another embodiment the liquid metal or thermally conductivefluid heat block can be thermally coupled to a Peltier-effectthermoelectric device.

In one embodiment the heat block is designed so that the liquid metal orthermally conductive fluid maintains a uniform temperature throughoutthe block.

The Multi-Zone Heater Device

In one embodiment the liquid metal or thermally conductive fluid heatblock is thermally coupled to a heating component, such as a multi-zoneheater and a bias cooling system. In one embodiment the bias coolingsystem provides a small constant flow of chilled coolant through biascooling channels in the attached to the base or sides of the heat block.This causes a constant, small heat loss from the heat block, which iscompensated by a multi-zone heater. The heater is thermally coupled tothe sample block for incubation segments where the temperature of thesample block maintained at a steady value. The constant small heat losscaused by the bias cooling flow allows the control system to implementproportional control both upward and downward in temperature in smallincrements. This means both heating and cooling at controlled,predictable, small rates is available to the temperature control systemto correct for block temperature errors. The multi-zone heater may becontrolled by a CPU.

In one embodiment, the heating element is comprised of one or more wirecomponents, such as heat coils (FIG. 10). Such wire components arearranged to provide optimum heating and to reduce or eliminate edgeeffects. For example, the wire elements are arranged at the perimeter ofthe heating block. Furthermore, where a plurality of wire elements areutilized, they are spaced equidistantly, or in a increasing/decreasingdistance gradient from the inside out to the outer perimeter to provideoptimum heating and reduce or eliminate edge effects. In one embodimentthe wires are arranged at the bottom of the block in a checkerboardpattern. In an alternative embodiment the wires are arranged inconcentric circles or ovals along the bottom of the heat block. Inanother embodiment the wires are arranged along the base and sides ofthe heat block. In yet another embodiment the wires are arranged inpattern which allows the liquid metal to flow around all sides of thewires, such as a suspended, stacked or 3 dimensional arrangementcomprising more than one checkerboard layer. In still another embodimentthe wires are located more closely together near the edges of the heatblock than in the interior of the heat block (such as variable spacing)so as to counteract the tendency of the outer edges of a heat block tocool at a faster rate than the interior (FIG. 10) It is known in the artthat edge effects result in discordance in temperature uniformity,usually at the outer perimeters of thermal units.

In one embodiment a coolant control system continuously circulates achilled liquid coolant such as a mixture of automobile antifreeze andwater through bias cooling channels attached to the heat block via inputand output tubes. The coolant control system also controls fluid flowthrough higher volume ramp cooling fluid flow paths in the heat block.The ramp cooling channels are used to rapidly change the temperature ofthe heat block by pumping large volumes of chilled liquid coolantthrough the block at a relatively high flow rate.

In one embodiment, the liquid coolant used to chill the heat blockconsists mainly of a mixture of water and ethylene glycol. The liquidcoolant is chilled by a heat exchanger which receives liquid coolantwhich has extracted heat from the sample block via an input tube. Theheat exchanger receives compressed liquid refrigerant (such as freon orethanol) via an input tube from a refrigeration unit. This refrigerationunit generally includes a compressor, a fan and a fin tube heatradiator. The refrigeration unit compresses refrigerant received fromthe heat exchanger. The heated refrigerant is cooled and condensed to aliquid in the fin tube condenser. The pressure of the refrigerant ismaintained above its vapor pressure in the fin tube condenser by a flowrestrictor capillary tube. The output of this capillary tube is coupledto the input of the heat exchanger. In the heat exchanger, the pressureof the refrigerant is allowed to drop below its vapor pressure, allowingit to expand. In this process of expansion, heat is absorbed from thewarmed liquid coolant circulating in the heat exchanger and this heat istransferred to the refrigerant thereby causing the refrigerant to boil.The warmed refrigerant is then extracted from the heat exchanger and iscompressed and again circulated through the fin tube condenser. The fanblows air through the fin tube condenser to cause heat in therefrigerant from tube to be exchanged with the ambient air. In oneembodiment the refrigeration is capable of extracting at least 400 wattsof heat at 30° C. and 100 watts of heat at 10° C. from the liquidcoolant to support the rapid temperature cycling.

In alternative embodiments, bias cooling may be eliminated or may besupplied by other means such as by the use of a cooling fan and coolingfins formed in the metal of the sample block, Peltier junctions orconstantly circulating water (such as distilled or tap water).

Peltier-Effect Thermoelectric Device.

Peltier devices or elements, also known as thermoelectric (TE) modules,are small solid-state devices that function as heat pumps. A typicalPeltier unit is a few millimeters thick by a few millimeters to a fewcentimeters square. It is a sandwich formed by two ceramic plates withan array of small Bismuth Telluride (Bi₂Te₃) cubes (“couples”) inbetween. When a DC current is applied heat is moved from one side of thedevice to the other where it can be removed by a heat sink. The “cold”side may be used to cool an electronic device such as a microprocessoror a photodetector. If the current is reversed the device changes thedirection in which the heat is moved. Peltier devices lack moving parts,do not require refrigerant, do not produce noise or vibration, are smallin size, have a long life, and are capable of precision temperaturecontrol. Temperature control may be provided by using a temperaturesensor feedback (such as a thermistor or a solid-state sensor) and aclosed-loop control circuit, which may be based on a general purposeprogrammable computer.

In an alternative embodiment a thermal cycler comprises a liquid metalor thermally conductive fluid heat block thermally coupled to a heatingcomponent which is a Peltier element, in order to obtain a desiredtemperature profile (a temperature curve during a defined time interval)in the liquid metal or thermally conductive fluid heat block (FIGS.1-4). In this embodiment the Peltier element, depending on thetemperature to be obtained, is used as a cooling or a heating elementwithin a temperature profile.

In another embodiment the thermal cycler may further comprise anelectric resistance heater and a Peltier element used in combination toobtain the required speed of the temperature changes in the liquid metalor thermally conductive fluid heat block and the required precision andhomogeneity of the temperature distribution.

In one embodiment the thermal cycler contains at least one Peltierelement that forms part of the thermal cycler for cyclic alteration ofthe temperature of a heat block comprising a liquid composition. Atleast one heat transfer surface of the Peltier element is in thermalcontact over a large area with the bottom surface of the liquid metal,heat block plate, or heat spreader and the other heat transfer surfaceis in contact over a large area with a cooling member for heatdissipation. The cooling member may be a metal such as aluminum orcopper. The thermal cycler may further comprise a fan for heatdissipation which may be optionally switchable. In an alternativeembodiment the liquid metal or thermally conductive fluid heat block anda Peltier element are joined to form a discrete unit (a swap block)which can be removed from the body of the thermal cycler. The swap blockmay further comprise a heat sink coupled to the Peltier element and/or afan. This swap block can be removed from the thermal cycler for repairor to be replaced by a swap block with different functional elements,such as receptacles designed to hold sample vessels of a different sizeor shape than the previous swap block. Further as technological advancesare made the swap blocks can be upgraded without purchasing an entirelynew thermal cycler.

In another embodiment, a heat block comprising a liquid composition isthermally coupled to a plurality of Peltier devices situated adjacentone another on a first side of said heat block. In an alternativeembodiment, a heat block comprising a liquid composition (501;551;571)is thermally coupled to a plurality of Peltier devices (503;553;573),wherein at least one Peltier device is situated on a first side of saidreservoir and at least a second Peltier device is situated on a secondside of said reservoir. In one embodiment at least one Peltier devicefrom a commercially available source, such as Marlow Industrries orNextreme Thermal Solutions is coupled to a heat block comprising aliquid composition (Nextreme Thermal Solutions; 3040 Cornwallis Road,P.O. Box 13981, Research Triangle Park, N.C. 27709-39810).

In one embodiment the Peltier element is protected from thermodynamicmechanical tension peaks by a central spring-biased securing means whichpresses the Peltier element and holds it against the heat block. ThePeltier element may be resiliently clamped between the heat transfersurfaces of the heat block and the cooling member. The contact surfaceof the cooling member can be pressed, for example, by a pressure spring,or similar device, against the Peltier element. In one embodiment thespring tension can be adjusted via a screw, a spring washer and a balland socket joint, which further increases the degrees of freedom of thecooling member.

In an alternative embodiment the Peltier element is used exclusively asa cold-producing (heat removal) element. That is, it is only used forcooling a heater unit. This will prolong the useful life of the Peltierelement.

In another embodiment, the thermal cycler may incorporate an electricresistance heater disposed around the heat block and along the peripheryof the outer wall of the heat block. In this embodiment the Peltierelement may be used only for cooling. This relieves the Peltier elementfrom mechanical thermal stress and thus contributes to prolonging theservice life of the Peltier element in the thermal cycler.

Lids

In some embodiments the liquid metal or thermally conductive fluid heatblock is part of a thermal cycler that optionally includes a lid, suchas a hinged lid. In various embodiments, a lid can be fastened to theblock by various means (e.g., clip, spring, screws, etc.). In oneembodiment the lid contains a closing and pressing device for securingthe sealed sample vessels positioned in the receptacle of the liquidmetal or thermally conductive fluid heat block. In an alternativeembodiment the lid may seal the sample vessels as it closes. A lid mayhave a spring held pressure plate, which presses each sample vessel witha defined force into the wells of the receptacle of the liquid metal orthermally conductive fluid heat block. The lid may further compriserecesses for holding the cap-shaped lids sample vessels and/or openingsfor piercing by pipetting needles in the pressure plate coaxially withthe sample vessels. The spring element may comprise a corrugated washer.In one embodiment a safety ring prevents the pressure plate from fallingout when the hinged lid is opened.

In another embodiment the lid comprises a heating element. In analternative embodiment the lid of the thermal cycler, incorporates adetection mechanism capable of detecting light. This lid may furthercomprise a heating element. For some analyses, such as PCR, it isnecessary to warm the receptacle to a controlled temperature. At theelevated temperature, the sample vessel contents tend to evaporate at ahigher rate. To reduce evaporation and consequent loss of material fromthe receptacle, it may be covered with a cover which is heated to abovethe temperature of the samples in the sample vessels contained in thereceptacle. In one embodiment the temperature of the cover is heated toa temperature at least 5° C. higher than the temperature of the samplevessel.

In one embodiment the heated lid comprises a cover that is sized tocover the entire top area of the receptacle. The lid may have at leasttwo thin plates made of rigid, heat tolerant material, such as ceramics,glass, or silicon rubber. Sandwiched between the plates is an electricalresistive heating element, which in one embodiment may be in the form ofa small diameter Nichrome wire or formed by depositing resistivematerials such as Nichrome or stannous oxide on one of the plates. Forexample, a 36 gauge Nichrome wire with a resistivity of 12 Ohms per footmay be used to provide sufficient heating to the cover. The heatingelement may be configured in a serpentine fashion across the area of theplate so as to provide uniform heating across the cover. A fillermaterial such as epoxy may be used to secure the plates and to fill thevoids between the plates.

In a related embodiment the heating element is connected to a variablepower supply, which can be controlled to provide current for heating thecover to a desired temperature. The leads between the power supply andthe heating element may be flexible and configured to avoid stress inthe leads so that the cover can be moved without restriction, e.g. by arobotic means in an automated laboratory workstation. A temperaturesensor may be provided on the cover to measure its temperature andprovide feedback for controlling the power supply for obtaining adesired temperature.

In an alternative embodiment it is contemplated that for situations inwhich the temperature of the sample vessels is below ambienttemperature, it may be desirable to cool the cover to a temperaturebelow ambient but above the temperature of the substance vapor. This isto maintain minimum temperature differential between the cover and thesubstance so that the temperature of the cover would not affect thecontrolled temperature of the substance in the receptacle.

Optical Assembly

In various aspects of the invention, the devices of the invention areconfigured to provide a means of measuring detectable labels in samplevessels comprising a reaction (e.g., real time PCR). Various embodimentsof the devices of the invention are fully compatible with detectionoptics, so that rapid nucleic acid amplification/detection can becarried out. The thermal cyclers of the present invention by providinguniform temperature, rapid temperatures and increased signalreflectivity, during PCR or related processes, enable more accurateamplification, detection and measurement. As such, one advantage is thatless expensive optical assemblies can be utilized with a thermal cyclerof the invention, and yet obtain as accurate or more accurate real-timemeasurements. Therefore, a thermal cycler of the invention enablesrapid, accurate, and reliable DNA amplification and detection, with lessexpensive optics, as well as conventional optic assemblies.

Optical measurement devices are known in the art. Generally, themeasuring optic includes a light source, which for example is formed bya light emitting diode. The light source is directed toward themeasuring field (e.g., sample vessel/tube). The light source iscontrolled by a evaluation and control circuit which can be operablylinked to a computer, containing computer executable logic forcontrolling optic measurements. The measuring optic further includes adetector which can receive light from the entire measuring field. Thedetector is connected with the evaluation circuit/computer.

Optical assemblies useful in various embodiments of the inventioncomprise those having a CCD imager, a CMOS imager, a line scanner, atleast one photodiode, at least one phototransistor, at least onephotomultiplier tube, at least one avalanche photodiode, a microlaser,or a q-switched laser. In various embodiments, the reader can be areflectance, transmission, epifluorescence/fluorescence,chemo-bioluminescence, magnetic or amperometry reader (or two or morecombinations), PIN diode, or other readers known in the art depending onthe signal that is to be detected from a sample tube.

In various embodiments, the light sources that can be coupled into anoptical assembly of the invention include LEDs, laser diodes, VCSELs,VECSELs, DPSS lasers or fiber optic connections that can be subsequentlycoupled to light sources such as large laser systems, laser diodes orlamps. In another embodiment, the diode is a laser diode. Laser diodescan be used for illumination, photodiode detectors have excellentsensitivity, and most materials have minimal autofluorescence in thepertinent spectral region. Any conventional, LED or photodiode may beutilized, such as the PIN photodiodes from Pacific Silicon Sensors (5700Corsa Avenue, Westlake Village Calif., 91362).

In various embodiments of the invention, optical assemblies areconfigured to provide excitation (light source)/emission (detector) atwavelengths such as: 365/460, 470/510, 530/555, 585/610, 625/660,680/712 nm. Furthermore, in some embodiments, various filter windows areutilized at +−5-20 nm. Various fluorescence filter sets are commerciallyavailable (e.g., Omega Filters; Omega Optical, Inc.; or INTORR),including dye-specific filters for single or multi-label fluorescence.

In some embodiments, an optical assembly is configured with lightsources having the specifications provided in Table 1:

Dominant wavelength (nm) Typical Luminous or CCT (K) or Radiant flux @Color Min. Max. 700 mA White 4500K 8000K 76 lm Royal Blue 455 nm 465 nm 385 mW Blue 465 nm 475 nm 28 lm Cyan 500 nm 510 nm 75 lm Green 520 nm535 nm 80 lm Amber 585 nm 595 nm 57 lm Red-Orange 610 nm 620 nm 86 lmRed 620 nm 635 nm 61 lm

FIG. 3 provides one example of an optical assembly, where a PINphotodiode is the optical detector. For example, the optical assemblyfor detecting fluorescence comprises a light source 603 that provideslights passing through an excitation filter 605 which is directed into asample vessel by a dichroic reflector/mirror 611 through an objectivelens 609 which focuses the light beam into the sample vessel. The samelens collects fluorescence generated by the constituents of the sample(e.g., SYBR Green or Cy5; intercalating dyes disclosed herein), whichemission passes the dichroic filter 611 and directed back up through abarrier filter 613, focus lens 615 and into the detector module PINphotodiode 617. The output is digitized and displayed as a graphelectronically or displayed on paper or recorded 619. Furthermore, theuse of epifluorescence provides an additional advantage in that thereare no size constraints, thus a numeric aperture aspheric or ball-typelenses can be used as a collection optic.

In further embodiments, additional excitation filters can be positionedfor increased spectral conditioning. In one embodiment, the lightsources is a Cree XLamp and the optical detector is a T5 and/or T18 PINdiode.

In one embodiment, an optical assembly emits and detects light throughthe same portion of a sample vessel (e.g., cap). In another embodiment,an optical assembly light source emits light from one portion of asample vessel (e.g., into a PCR reaction), while emissions are detectedfrom another portion of the sample vessel (e.g., where light source isat bottom and detector is at top, or vice versa).

In one embodiment, the reader is a LED reader which detects afluorescence signal. The fluorescence signal is excited by a lightemitting diode that emits in the region of the optical spectrum andwithin the absorbance peak of the signal (e.g., fluorescent label). Theemitted fluorescence signal is detected by a photodiode. Furthermore,the wavelength of the signal detected may be limited using a long passfilter which blocks stray emitted light and transmits light withwavelengths at and above the peak emission wavelength of thefluorescence emitting label. In other embodiments, the long pass filtermay be replaced by a band pass filter. Furthermore, the excitation lightmay be limited by a band pass filter.

In some embodiments the excitation source and the detector are mountedin a single machine (such as the body of a thermal cycler), molded block(e.g., FIGS. 1-2), for simplified reading of the fluorescent signalsgenerated in the sample tubes.

For example, Cy5 is a popular red-emitting fluorophore with a very highextinction coefficient. Common forms of such a fluorophore include theN-hydroxysuccinimide ester of or the related dye, Cy5.5. These dyes areindodicarbocyanine dyes that are used commonly in flow cytometry andautomated fluorescence sequencers and are available from Amersham(Pittsburgh, Pa.). Cy5 is commercially available as amidites for direct,automated incorporation into oligonucleotides. In one embodiment,samples labeled with Cy5 are processed utilizing the devices of theinvention. For example, working in the red/infrared region of thespectrum is advantageous when choosing optical components forinstrumentation.

In another example real-time measurements of PCR amplification can bemade utilizing SYBR Green. However, it should be noted that as desired,in some embodiments, any of the various labels/dyes known in the art ordisclosed herein can be utilized in thermal cycler devices of theinvention (e.g., SYBR Green, Q-dots, etc.).

In various embodiments of the invention, a system comprising a cycler ofthe invention further comprises a collection of photodetectors, in whicheach photodetector provides an output signal. The system also comprisesat least one light source. The light source is positioned such thatlight emitted passes through a corresponding well retained in orotherwise provided by a multi-well plate (305;405) or strip of samplevessels and to a corresponding photodetector or a collection ofphotodetectors. The system also includes a processor or other means foranalyzing the output signals from the plurality of photodetectors. In analternative embodiment, the devices of the invention obviate the need toutilize expensive fluorochromes or dye markers, which require largeintegrated light sources and detection optics on the system. Forexample, an integrated real-time PCR system can cost $90,000 (AppliedBiosystems ABI PRISM® 7700 Sequence Detection System) as compared to$7,500 for a non-real time PCR system (GeneAmp 9700). Both systemsperform PCR amplification for 96 wellplates but the GeneAmp 9700requires a separate spectrophotometer or a fluorescent wellplate readerfor DNA concentration measurement.

Since the footprint of an LED or laser diode is very small, multipleLEDs or lasers of different wavelength could be integrated into a singlepackage or several packaged LEDs/laser can be very closely spaced toexcite one well/sample tube.

In some embodiments, the LED actually represents several LEDs withdifferent wavelengths, but very closely spaced. Therefore, in furtherembodiments, the detectors are similarly configured.

In some embodiments, light sources for optics configurations of theinvention can be an LED or a laser diode. Other light sources can beutilized. Furthermore, the number of light sources used in associationwith each well may vary. In one non limiting example of using devices ofthe invention, an LED is activated to emit light of a first wavelengthor first set of wavelengths, which excites a dye or label in a samplethat which emits a signal. The signal is detected by the appropriatephotodetector and then, or concurrently, a second LED is activated,which emits light having a different wavelength or set of wavelengthsfrom the first LED. This light excites a different dye or label in asample, which emits a signal that is detected by the appropriatephotodetector. The second LED is de-activated and then, or concurrently,a third LED is activated. The third LED emits light having a differentwavelength or set of wavelengths from the first LED and second LED. Thislight excites a different dye or label in a sample, which emits a signalthat is detected by the appropriate photodetector. These measurementsare performed very rapidly and processed by a computer generateddisplay. The collection of closely spaced light sources can beconfigured to sequentially emit light as described.

In other embodiments, different light sources are configured in theoptical assembly and separately detected using optical detectors,wherein detection is at the same time.

In one embodiment, the devices of the invention are configured with anarray of light sources and light detectors. It will be understood thatthe light source array includes a plurality of light sources disposed ona suitable substrate or mounting component and arranged in a particularconfiguration, which typically is a grid pattern. The well arraycomprises a plurality of sample wells (FIG. 1, 2), also supported andpositioned on or within a suitable retaining substrate. Thephotodetector array includes a plurality of photodetectors similarlymounted and arranged to receive light emitted from an array of samplevessels (305;405) such as through sample vessel caps (303;403) (FIG. 3).

In some embodiments, a rail system comprising multiple separate lightsources (of the same or multiple different wavelengths) can beconfigured over a row of samples in a multi-row arrangement, along withthe corresponding number of detectors. For example, the number of lightsources and corresponding detectors can be 8 separate light sources ofperhaps multiple wavelengths, detected by 8 different detector setupeach which can detect multiple wavelengths emitted from an excitedsample. Therefore, the rail system can be operated to move back andforth interrogating successive rows of sample vessels. Variouscommercially available filters can be utilized as described hereinabove. In one embodiment the detectors comprise optics made cheaplythrough injection molding.

In some embodiments, higher power LED's can be used. Avalanchephotodiodes, e.g. SiC, GaN, GaAs or Si or blue enhance Si photodiodescan also be used. The sensitivity of avalanche photodiodes is muchgreater than simple photodiodes because the signal is amplified by theavalanche process. Avalanche photodiodes have a typical gain of between10 and 10000, which means that the signal is amplified by a factor of 10to 10000. Using improved measurement techniques like lock-in amplifierscan also extend the dynamic range of the measurements.

In one embodiment of a PCR system utilizing light sources andparticularly the use of LED for the emission of such light, provides newpossibilities and applications. In one embodiment, an LED light sourcecontemplated is a GaN-based ultra-violet LED. In another embodiment, thelight source is cree xlamp 750 mwatt ultra bright LEDs. In oneembodiment, a single wavelength emission is utilized. No additionalgrating or filter or complex optics are required to select the desiredwavelength and focus the light. That significantly simplifies theexperimental setup and reduces the cost of assembly. Another advantageis the low cost of LED's. Semiconductor LED's can be mass-produced andmade extremely inexpensive. Current GaN-based violet, blue and greenLED's cost on the order of 10 to 50 cents per packaged device and asimilar price range is to be expected for future mass-produced GaN-basedLED's. Multiple wavelength LED's can be either integrated as hybrid LEDchips or special LED's could be developed, whose emission can beswitched between two or more wavelengths.

Yet another advantage relates to the high output power of LED's. LED'soutput power levels in the range of 10 mW are within reach in the nearfuture. Furthermore, the typical footprint of an LED is 200 um×200 um,which means that the light intensity can be concentrated to a smallerarea and reduces the amount of additional optics (e.g. lenses) needed toconcentrate the light. That is a considerable advantage for highthroughput PCR systems with a large number of wells per plate (48, 96,384, or 1536 wells) and consequently smaller wells. Even with 48, 96 or384 wells, well dimensions are still large enough to fit several LEDs inthe area of a single well in a wellplate.

Furthermore, another advantage relates to LED arrays. Multiple LED's canalso be arranged in one- or two-dimensional LED arrays. This enables themeasurement of the fluorescence in multiple wells at the same time.Massive parallel processing significantly reduces the measurement timeand accelerates the throughput. This can be a significant cost/timefactor in the operation of a PCR system, particularly with the trendgoing to higher-density wellplates.

Moreover, another advantage of LED's is that these light sources can bepulsed. In order to avoid bleaching or heating of the DNA molecules;short, but intense pulses can be produced by LED's. LED's can be turnedon and off in a very short time scale (about 1 ns to 100 ns), dependingon the design, the size and the packaging of the LED. The LED pulses canalso be synchronized with a photodetector readout using common lock-intechniques to achieve better signal to noise ratios and highersensitivity ranges. In addition, LED's do not require any warm-up timebefore stable light output is achieved. This is in contrast to deuteriumand Xenon lamps, which require at least several minutes of warm-up time,before stable operation is achieved.

Yet another advantage in using an LED light emitting source is therelatively long operating lives of such components. It is believed thatthe operating life of an LED may be as long as 10,000 or more hours. Theuse of these light sources would eliminate replacement of the LED inmost systems.

In one embodiment, a method of performing a polymerase chain reactionassay with fluorescence detection is provided. The method comprisesproviding a system that includes a multi-well plate, a thermal cycler, aphotodetector that provides an output signal, at least one light sourcepositioned to pass light through the multi-well plate and to thephotodetector, and a means for analyzing the output signal of thephotodetector. The method also comprises obtaining samples upon whichthe polymerase chain reaction assay is to be performed. Additionally,the method comprises depositing samples in the multi-well plate. And,the method comprises performing a polymerase chain reaction in thesamples. The method includes emitting light from the light source(s)such that light passes through the samples to the photodetector. And,the method comprises analyzing the output of the photodetector todetermine the absorbance of emitted fluorescent light and informationindicative of the polymerase chain reaction.

In another embodiment the fluorescence emitted by a sample after PCR wasperformed in a thermal cycler comprising a heat block comprising aliquid composition is detected using rough detection. In an embodimentthe rough detection does not quantitate the amount of an amplificationproduct or amplicon, but instead only detects the presence or absence ofsaid amplification product. Rough detection may be performed usinginexpensive optics or detectors, with few or no filters and/or plasticlens. In on embodiment only a photodiode or LED detector is used. Inanother embodiment, fluorescence is detected using a filterless system,such as time resolved fluorescence (TRF). In one aspect the light source(LED or laser diode) is turned off, and the fluorescent moleculescontinue to emit light for a short but measurable amount of time; thisemitted light can be measured without having to filter out the LED/laserlight.

In yet another embodiment a detection system is used with FRET-basedprobes. In an embodiment, the detection system is capable of detectingtwo different wavelengths nearly simultaneously. With FRET probes, twofluorophores are located on the probe. A sample comprising the probe isstimulated with a single excitation light source. The light source is ofa wavelength that stimulates a first fluorophore, which emits light, themajority of which is absorbed by the second, neighboring fluorophore.The second fluorophore emits light at a wavelength different from thefirst fluorophore. Both of these signals are then detected.

In accordance with yet another aspect of the present exemplaryembodiment, a method of performing a polymerase chain reaction assay isprovided. The method is based upon using light as follows. The methodincludes providing a system including (i) a multi-well plate adapted toretain a plurality of samples, (ii) a thermal cycler, (iii) aphotodetector that provides an output signal, (iv) a plurality of lightsources positioned such that light emitted passes through the multi-wellplate to the photodetector, and (v) a means for analyzing the outputsignal of the photodetector upon detecting ultra-violet light. Themethod also comprises obtaining samples upon which the polymerase chainreaction assay is to be performed. The method further comprisesdepositing the samples in the multi-well plate. The method alsocomprises performing a polymerase chain reaction in the samples. Themethod further comprises emitting light from the plurality of lightsources such that the light passes through the samples to thephotodetector. The method also includes analyzing the output signal ofthe photodetector.

In various embodiments turn on/off times for LEDs are typically on theorder of a few nanoseconds or tens of nanoseconds. In other embodiments,laser diodes are even faster with sub nanosecond switching times.

In an alternative embodiment, a PCR system is provided and relatedassays and techniques that do not require the use of fluorophores andassociated detection light sources and optics otherwise required. Forexample, LED could contain a 260 nm and a 280 nm LED. To perform anabsorbance measurement, first the 260 nm LED would be turned on and theabsorbed light at 260 nm detected by the photodetector. The 260 nm LEDwould be turned off and then the 280 nm would be turned on and theabsorbed light at 280 nm detected by the photodetector. Thesemeasurements could be performed very quickly after each other since theydo not require any physical movement of the sample. LEDs can be turnedon and off very quickly. Therefore, in one alternative embodiment theoptical configuration can reduce the cost of fluorescent primers andTaqman probes utilized with many real-time PCR systems.

In one embodiment, an array of inexpensive ultra-violet LED's, emitting260 nm and 280 nm wavelength light are incorporated in a PCR system withthe format of a wellplate in thermal contact (directly/indirectly) witha liquid medium (e.g., liquid metal or a thermal fluid). The arrays ofemitter and detectors have a configuration, that may correspond to thearrangement of sample vessels in the liquid composition heat block ofthe thermal cycler, for example, like the sample vessels (305;405) inFIG. 3. Thus, a plurality of ultra-violet light emitting units, such asLED's are positioned with respect to a plurality of wells FIG. 1, suchthat light emitted from each LED travels through a corresponding well(and sample contained therein), and is received by a correspondingphotoreceptor or photodetector. Optical filters could be used, eitherplaced at the input of the photodetector or at the output of theLEDs/lasers or both to suppress any unwanted light (e.g. light emittedby the LED aside from the center wavelength peak) FIG. 3. For example,LEDs sometimes exhibit luminescence at longer wavelengths fromrecombination through defects in the LEDs active regions orrecombination of carriers outside the active region of the LED. Thisunwanted luminescence is typically 3 to 4 orders smaller than the mainluminescence peak. Nevertheless it may be desirable to suppress thisluminescence even further by using optical band-pass filters.

In various embodiments optical assembly systems known in the art can beconfigured for use with a thermal cycler device of the invention.Examples of such optical assemblies as well as reagents useful indetecting reaction products are disclosed in US Patent Application Nos.2006/0134644, 2006/0014200, 2005/0255516, 2005/0237524, 2005/0136448,2004/0133724, 2003/0059822, 2002/0034746 and U.S. Pat. Nos. 7,101,509,6,942,971, 6,940,598, 6,911,327, 6,783,934, 6,713,297, 6,403,037,6,369,893, 7,122,799, 7,113,624, 6,037,130, 5,792,610, 5,440,388,6,873,417, 6,998,598, 6,437,345, 53,011,059, and 6,388,799, thedisclosures of each of which is incorporated by reference herein in itsentirety.

Control Assembly

In various embodiments a control assembly is operatively linked to athermal cycler of the invention. Such a control assembly, for example,comprises a programmable computer comprising computer executable logicthat functions to operate any aspect of the devices, methods and/orsystems of the invention. For example, the control assembly can turnon/off motors, fans, heating components, stir bars, continuous flowdevices and optical assemblies. The control assembly can be programmedto automatically process samples, run multiple PCR cycles, obtainmeasurements, digitize measurements into data, convert data intocharts/graphs and report.

Computers for controlling instrumentation, recording signals, processingand analyzing signals or data can be any of a personal computer (PC),digital computers, a microprocessor based computer, a portable computer,or other type of processing device. Generally, a computer comprises acentral processing unit, a storage or memory unit that can record andread information and programs using machine-readable storage media, acommunication terminal such as a wired communication device or awireless communication device, an output device such as a displayterminal, and an input device such as a keyboard. The display terminalcan be a touch screen display, in which case it can function as both adisplay device and an input device. Different and/or additional inputdevices can be present such as a pointing device, such as a mouse or ajoystick, and different or additional output devices can be present suchas an enunciator, for example a speaker, a second display, or a printer.The computer can run any one of a variety of operating systems, such asfor example, any one of several versions of Windows, or of MacOS, or ofUnix, or of Linux.

In some embodiments, the control assembly executes the necessaryprograms to digitize the signals detected and measured from reactionvessels and process the data into a readable form (e.g., table, chart,grid, graph or other output known in the art). Such a form can bedisplayed or recorded electronically or provided in a paper format.

In some embodiments, the control assembly controls circuitry linked tothe thermal elements so as to regulate/control cycles temperatures of athermal cycler of the invention.

In further, embodiments, the control assembly generates the samplingstrobes of the optical assembly, the rate of which is programmed to runautomatically. Of course it will be apparent, that such timing isadjustable for shining a light sources and operating a detector todetect and measure signals (e.g., fluorescence).

In another embodiment an apparatus comprising a control assembly furthercomprises a means for moving sample vessels into apertures, such aswells in the receptacle of a heat block comprising a liquid composition.In an embodiment said means could be a robotic system comprising motors,pulleys, clamps and other structures necessary for moving samplevessels.

Sample preparation station. In some aspects of the invention, thedevices/systems of the invention are operatively linked to a roboticssample preparation and/or sample processing unit. For example, a controlassembly can provide a program to operate automated collection ofsamples, adding of reagents to collection tubes, processing/extractingnucleic acids from said tubes, optionally transferring samples to newtubes, adding necessary reagents for a subsequent reaction (e.g., PCR orsequencing), and transferring samples to a thermal cycler, which aredescribed herein. In various embodiments, the sample preparation can bein a continuous flow PCR system described herein (FIG. 11) or in anon-continuous systems (FIG. 1, 5).

Methods of Performing PCR

A thermal cycler comprising a liquid metal or a thermally conductivefluid heat block can be used for disease diagnosis, drug screening,genotyping individuals, phylogenetic classification, environmentalsurveillance, parental and forensic identification amongst other uses.Further, nucleic acids can be obtained from any source forexperimentation using a liquid metal or a thermally conductive fluidheat block. For example, a test sample can be biological and/orenvironmental samples. Biological samples may be derived from human,other animals, or plants, body fluid, solid tissue samples, tissuecultures or cells derived therefrom and the progeny thereof, sections orsmears prepared from any of these sources, or any other samplessuspected to contain the target nucleic acids. Exemplary biologicalsamples are body fluids including but not limited to blood, urine,spinal fluid, cerebrospinal fluid, synovial fluid, semen, and saliva.Other types of biological sample may include food products andingredients such as vegetables, dairy items, meat, meat by-products, andwaste. Environmental samples are derived from environmental materialincluding but not limited to soil, water, sewage, cosmetic,agricultural, industrial samples, air filter samples, and airconditioning samples.

A thermal cycler comprising a liquid metal or a thermally conductivefluid heat block can be used in any protocol or experiment that requireseither thermal cycling or a heat block that can accurately maintain auniform temperature. For example said thermal cycler can be used forpolymerase chain reaction (PCR), quantitative polymerase chain reaction(qPCR), nucleic acid sequencing, ligase chain polymerase chain reaction(LCR-PCR), reverse transcription PCR reaction (RT-PCR), single baseextension reaction (SBE), multiplex single base extension reaction(MSBE), reverse transcription, and nucleic acid ligation.

The apparatus of this invention allows one to perform PCR with increasedspeed and specificity, particularly in the context of real time PCR. Theuse of a composition with high thermal conductivity, such as a liquidmetal, allows one to perform temperature ramping (both up and down) muchfaster than traditional PCR. This not only increases the potential speedat which one can carry out PCR, but it also increases the specificity ofPCR by decreasing the incidence of non-specific hybridization ofprimers. Furthermore, in the context of real time PCR, measuring signalfrom a discrete portion of the test receptacle, such as the top,relieves one of the need to remove sample vessels from the heatingcomposition for measurement. This also preserves temperature control andallows measurements to be made in real time with the heating cycles. Theuse of a reflecting material that prevents escape of signal except fromthe discrete location allows less sensitive detectors to be used as morelight can be collected for measurement.

PCR reaction conditions typically comprise either two or three stepcycles. Two step cycles have a denaturation step followed by ahybridization/elongation step. Three step cycles comprise a denaturationstep followed by a hybridization step during which the primer hybridizesto the strands of DNA, followed by a separate elongation step. Thepolymerase reactions are incubated under conditions in which the primershybridize to the target sequences and are extended by a polymerase. Theamplification reaction cycle conditions are selected so that the primershybridize specifically to the target sequence and are extended.

Successful PCR amplification requires high yield, high selectivity, anda controlled reaction rate at each step. Yield, selectivity, andreaction rate generally depend on the temperature, and optimaltemperatures depend on the composition and length of the polynucleotide,enzymes and other components in the reaction system. In addition,different temperatures may be optimal for different steps. Optimalreaction conditions may vary, depending on the target sequence and thecomposition of the primer. Thermal cyclers may be programmed byselecting temperatures to be maintained, time durations for each cycle,number of cycles, rate of temperature change and the like.

Primers for amplification reactions can be designed according to knownalgorithms. For example, algorithms implemented in commerciallyavailable or custom software can be used to design primers foramplifying desired target sequences. Typically, primers can range arefrom least 12 bases, more often 15, 18, or 20 bases in length but canrange up to 50+ bases in length. Primers are typically designed so thatall of the primers participating in a particular reaction have meltingtemperatures that are within at least 5° C., and more typically within2° C. of each other. Primers are further designed to avoid priming onthemselves or each other. Primer concentration should be sufficient tobind to the amount of target sequences that are amplified so as toprovide an accurate assessment of the quantity of amplified sequence.Those of skill in the art will recognize that the amount ofconcentration of primer will vary according to the binding affinity ofthe primers as well as the quantity of sequence to be bound. Typicalprimer concentrations will range from 0.01 uM to 0.5 uM.

In one embodiment, the liquid metal or thermally conductive fluidheating block may be used for PCR, either as part of a thermal cycler oras a heat block used to maintain a single temperature. In a typical PCRcycle, a sample comprising a DNA polynucleotide and a PCR reactioncocktail is denatured by treatment in a liquid metal or thermallyconductive fluid heat block at about 90-98° C. for 10-90 seconds. Thedenatured polynucleotide is then hybridized to oligonucleotide primersby treatment in a liquid metal or thermally conductive fluid heat blockat a temperature of about 30-65° C. for 1-2 minutes. Chain extensionthen occurs by the action of a DNA polymerase on the polynucleotideannealed to the oligonucleotide primer. This reaction occurs at atemperature of about 70-75° C. for 30 seconds to 5 minutes in the liquidmetal or thermally conductive fluid heat block. Any desired number ofPCR cycles may be carried out depending on variables including but notlimited to the amount of the initial DNA polynucleotide, the length ofthe desired product and primer stringency.

In another embodiment, the PCR cycle comprises denaturation of the DNApolynucleotide at a temperature of 94° C. for about 1 minute. Thehybridization of the oligonucleotide to the denatured polynucleotideoccurs at a temperature of about 37°-65° C. for about one minute. Thepolymerase reaction is carried out for about one minute at about 72° C.All reactions are carried out in a multiwell plate which is insertedinto the wells of a receptacle in a liquid metal or thermally conductivefluid heat block. About 30 PCR cycles are performed. The abovetemperature ranges and the other numbers are not intended to limit thescope of the invention. These ranges are dependant on other factors suchas the type of enzyme, the type of container or plate, the type ofbiological sample, the size of samples, etc. One of ordinary skill inthe art will recognize that the temperatures, time durations and cyclenumber can readily be modified as necessary.

Reverse Transcription PCR

Revere transcription refers to the process by which mRNA is copied tocDNA by a reverse transcriptase (such as Moloney murine leukemia virus(MMLV) transcriptase Avian myeloblastosis virus (AMV) transcriptase or avariant thereof) composed using an oligo dT primer or a random oligomers(such as a random hexamer or octamer). In real-time PCR, a reversetranscriptase that has an endo H activity is typically used. Thisremoves the mRNA allowing the second strand of DNA to be formed. Reversetranscription typically occurs as a single step before PCR. In oneembodiment the RT reaction is performed in a liquid metal or thermallyconductive fluid heat block by incubating an RNA sample a transcriptasethe necessary buffers and components for about an hour at about 37° C.,followed by incubation for about 15 minutes at about 45° C. followed byincubation at about 95° C. The cDNA product is then removed and used asa template for PCR. In an alternative embodiment the RT step is followedsequentially by the PCR step, for example in a one-step PCR protocol. Inthis embodiment all of the reaction components are present in the samplevessel for the RT step and the PCR step. However, the DNA polymerase isblocked from activity until it is activated by an extended incubation at95° C. for 5-10 minutes. In one embodiment the DNA polymerase is blockedfrom activity by the presence of a blocking antibody that is permanentlyinactivated during the 95° C. incubation step.

Real Time PCR

In molecular biology, real-time polymerase chain reaction, also calledquantitative real time polymerase chain reaction (QRT-PCR) or kineticpolymerase chain reaction, is used to simultaneously quantify andamplify a specific part of a given DNA molecule. It is used to determinewhether or not a specific sequence is present in the sample; and if itis present, the number of copies in the sample. It is the real-timeversion of quantitative polymerase chain reaction (Q-PCR), itself amodification of polymerase chain reaction.

The procedure follows the general pattern of polymerase chain reaction,but the DNA is quantified after each round of amplification; this is the“real-time” aspect of it. In one embodiment the DNA is quantified by theuse of fluorescent dyes that intercalate with double-strand DNA. In analternative embodiment modified DNA oligonucleotide probes thatfluoresce when hybridized with a complementary DNA are used to quantifythe DNA.

In another embodiment real-time polymerase chain reaction is combinedwith reverse transcription polymerase chain reaction to quantify lowabundance messenger RNA (mRNA), enabling a researcher to quantifyrelative gene expression at a particular time, or in a particular cellor tissue type.

In certain embodiments, the amplified products are directly visualizedwith detectable label such as a fluorescent DNA-binding dye. In oneembodiment the amplified products are quantified using an intercalatingdye, including but not limited to SYBR green, SYBR blue, DAPI, propidiumiodine, Hoeste, SYBR gold, ethidium bromide, acridines, proflavine,acridine orange, acriflavine, fluorcoumanin, ellipticine, daunomycin,chloroquine, distamycin D, chromomycin, homidium, mithramycin, rutheniumpolypyridyls, anthramycin. For example, a DNA binding dye such as SYBRGreen binds all double stranded (ds) DNA and an increase in fluorescenceintensity is measured, thus allowing initial concentrations to bedetermined. A standard PCR reaction cocktail is prepared as usual, withthe addition of fluorescent dsDNA dye and added to a sample. Thereaction is then run in a liquid heatblock thermal cycler, and aftereach cycle, the levels of fluorescence are measured with a camera. Thedye fluoresces much more strongly when bound to the dsDNA (i.e. PCRproduct). Because the amount of the dye intercalated into thedouble-stranded DNA molecules is typically proportional to the amount ofthe amplified DNA products, one can conveniently determine the amount ofthe amplified products by quantifying the fluorescence of theintercalated dye using the optical systems of the present invention orother suitable instrument in the art. When referenced to a standarddilution, the dsDNA concentration in the PCR can be determined. In someembodiments the results obtained for a sequence of interest may benormalized against a stably expressed gene (“housekeeping gene”) such asactin, GAPDH, or 18s rRNA.

In various embodiments, labels/dyes detected by systems or devices ofthe invention. The term “label” or “dye” refers to any substance whichis capable of producing a signal that is detectable by visual orinstrumental means. Various labels suitable for use in the presentinvention include labels which produce signals through either chemicalor physical means, such as fluorescent dyes, chromophores,electrochemical moieties, enzymes, radioactive moieties, phosphorescentgroups, fluorescent moieties, chemiluminescent moieties, or quantumdots, or more particularly, radiolabels, fluorophore-labels, quantumdot-labels, chromophore-labels, enzyme-labels, affinity ligand-labels,electromagnetic spin labels, heavy atom labels, probes labeled withnanoparticle light scattering labels or other nanoparticles, fluoresceinisothiocyanate (FITC), TRITC, rhodamine, tetramethylrhodamine,R-phycoerythrin, Cy-3, Cy-5, Cy-7, Texas Red, Phar-Red, allophycocyanin(APC), probes such as Taqman probes, TaqMan Tamara probes, TaqMan MGBprobes or Lion probes (Biotools), fluorescent dyes such as SYBR Green I,SYBR Green II, SYBR gold, CellTracker Green, 7-AAD, ethidium homodimerI, ethidium homodimer II, ethidium homodimer III or ethidium bromide,epitope tags such as the FLAG or HA epitope, and enzyme tags such asalkaline phosphatase, horseradish peroxidase, I²-galactosidase, alkalinephosphatase, β-galactosidase, or acetylcholinesterase and haptenconjugates such as digoxigenin or dinitrophenyl, or members of a bindingpair that are capable of forming complexes such as streptavidin/biotin,avidin/biotin or an antigen/antibody complex including, for example,rabbit IgG and anti-rabbit IgG; fluorophores such as umbelliferone,fluorescein, fluorescein isothiocyanate, rhodamine, tetramethylrhodamine, eosin, green fluorescent protein, erythrosin, coumarin,methyl coumarin, pyrene, malachite green, stilbene, lucifer yellow,Cascade Blue, dichlorotriazinylamine fluorescein, dansyl chloride,phycoerythrin, fluorescent lanthanide complexes such as those includingEuropium and Terbium, Cy3, Cy5, molecular beacons and fluorescentderivatives thereof, a luminescent material such as luminol; lightscattering or plasmon resonant materials such as gold or silverparticles or quantum dots; or radioactive material including ¹⁴C, ¹²³I,¹²⁴I, ¹²⁵I, ¹³¹I, ^(99m)Tc, ³⁵S or ³H; or spherical shells, and probeslabeled with any other signal generating label known to those of skillin the art. For example, detectable molecules include but are notlimited to fluorophores as well as others known in the art as described,for example, in Principles of Fluorescence Spectroscopy, Joseph R.Lakowicz (Editor), Plenum Pub Corp, 2nd edition (July 1999) and the6^(th) Edition of the Molecular Probes Handbook by Richard P. Hoagland.

Intercalating dyes are detected using the devices of the inventioninclude but are note limited to phenanthridines and acridines (e.g.,ethidium bromide, propidium iodide, hexidium iodide, dihydroethidium,ethidium homodimer-1 and -2, ethidium monoazide, and ACMA); some minorgrove binders such as indoles and imidazoles (e.g., Hoechst 33258,Hoechst 33342, Hoechst 34580 and DAPI); and miscellaneous nucleic acidstains such as acridine orange (also capable of intercalating), 7-AAD,actinomycin D, LDS751, and hydroxystilbamidine. All of theaforementioned nucleic acid stains are commercially available fromsuppliers such as Molecular Probes, Inc.

Still other examples of nucleic acid stains include the following dyesfrom Molecular Probes: cyanine dyes such as SYTOX Blue, SYTOX Green,SYTOX Orange, POPO-1, POPO-3, YOYO-1, YOYO-3, TOTO-1, TOTO-3, LOLO-1,BOBO-1, BOBO-3, PO-PRO-1, PO-PRO-3, BO-PRO-1, BO-PRO-3, TO-PRO-1,TO-PRO-3, TO-PRO-5, JO-PRO-1, LO-PRO-1, YO-PRO-1, YO-PRO-3, PicoGreen,OliGreen, RiboGreen, SYBR Gold, SYBR Green I, SYBR Green II, SYBR DX,SYTO-40, -41, -42, -43, -44, -45 (blue), SYTO-13, -16, -24, -21, -23,-12, -11, -20, -22, -15, -14, -25 (green), SYTO-81, -80, -82, -83, -84,-85 (orange), SYTO-64, -17, -59, -61, -62, -60, -63 (red). Otherdetectable markers include chemiluminescent and chromogenic molecules,optical or electron density markers, etc.

As noted above in certain embodiments, labels comprise semiconductornanocrystals such as quantum dots (i.e., Qdots), described in U.S. Pat.No. 6,207,392. Qdots are commercially available from Quantum DotCorporation. The semiconductor nanocrystals useful in the practice ofthe invention include nanocrystals of Group II-VI semiconductors such asMgS, MgSe, MgTe, CaS, CaSe, CaTe, SrS, SrSe, SrTe, BaS, BaSe, BaTe, ZnS,ZnSe, ZnTe, CdS, CdSe, CdTe, HgS, HgSe, and HgTe as well as mixedcompositions thereof; as well as nanocrystals of Group III-Vsemiconductors such as GaAs, InGaAs, InP, and InAs and mixedcompositions thereof. The use of Group IV semiconductors such asgermanium or silicon, or the use of organic semiconductors, may also befeasible under certain conditions. The semiconductor nanocrystals mayalso include alloys comprising two or more semiconductors selected fromthe group consisting of the above Group III-V compounds, Group II-VIcompounds, Group IV elements, and combinations of same.

In addition to various kinds of fluorescent DNA-binding dye, otherluminescent labels such as sequence specific probes can be employed inthe amplification reaction to facilitate the detection andquantification of the amplified product. Probe based quantitativeamplification relies on the sequence-specific detection of a desiredamplified product. Unlike the dye-based quantitative methods, itutilizes a luminescent, target-specific probe (e.g., TaqMan® probes)resulting in increased specificity and sensitivity. Methods forperforming probe-based quantitative amplification are well establishedin the art and are taught in U.S. Pat. No. 5,210,015.

In another embodiment fluorescent oligonucleotide probes are used toquantify the DNA. Fluorescent oligonucleotides (primers or probes)containing base-linked or terminally-linked fluors and quenchers arewell-known in the art. They can be obtained, for example, from LifeTechnologies (Gaithersburg, Md.), Sigma-Genosys (The Woodlands, Tex.),Genset Corp. (La Jolla, Calif.), or Synthetic Genetics (San Diego,Calif.). Base-linked fluors are incorporated into the oligonucleotidesby post-synthesis modification of oligonucleotides that are synthesizedwith reactive groups linked to bases. One of skill in the art willrecognize that a large number of different fluorophores are available,including from commercial sources such as Molecular Probes, Eugene,Oreg. and other fluorophores are known to those of skill in the art.Useful fluorophores include: fluorescein, fluorescein isothiocyanate(FITC), carboxy tetrachloro fluorescein (TET), NHS-fluorescein, 5 and/or6-carboxy fluorescein (FAM), 5-(or 6-) iodoacetamidofluorescein,5-{[2(and 3)-5-(Acetylmercapto)-succinyl]amino} fluorescein(SAMSA-fluorescein), and other fluorescein derivatives, rhodamine,Lissamine rhodamine B sulfonyl chloride, Texas red sulfonyl chloride, 5and/or 6 carboxy rhodamine (ROX) and other rhodamine derivatives,coumarin, 7-amino-methyl-coumarin, 7-Amino-4-methylcoumarin-3-aceticacid (AMCA), and other coumarin derivatives, BODIPY™ fluorophores,Cascade Blue™ fluorophores such as 8-methoxypyrene-1,3,6-trisulfonicacid trisodium salt, Lucifer yellow fluorophores such as3,6-Disulfonate-4-amino-naphthalimide, phycobiliproteins derivatives,Alexa fluor dyes (available from Molecular Probes, Eugene, Oreg.) andother fluorophores known to those of skill in the art. For a generallisting of useful fluorophores, see also Hermanson, G. T., BIOCONJUGATETECHNIQUES (Academic Press, San Diego, 1996).

Embodiments using fluorescent reporter probes produce accurate andreliable results. Sequence specific RNA or DNA based probes are used tospecifically quantify the probe sequence and not all double strandedDNA. This also allows for multiplexing—assaying for several genes in thesame reaction by using specific probes with different-colored labels.

In one embodiment PCR is carried out in a thermal cycler comprising athe liquid metal or thermally conductive fluid heat block comprising aliquid composition. In an embodiment, the thermal cycler furthercomprises an optical assembly. In another embodiment the liquid metal orthermally conductive fluid heat block rapidly and uniformly modulatesthe temperature of samples contained within sample vessels to allowdetection of amplification products in real time. In another embodimentthe detection is via a non-specific nucleic acid label such as anintercalating dye, wherein the signal index, or the positivefluorescence intensity signal generated by a specific amplificationproduct is at least 3 times the fluorescence intensity generated by aPCR control sample, such as about 3.5, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8,8.5, 9, 9.5, 10, 10.5, or 11. In an embodiment the thermal cycler maymodulate the sample temperature by more than 10° C. per second, such as10.5° C. per second.

In one embodiment an RNA based probe with a fluorescent reporter and aquencher held in adjacent positions is used. The close proximity of thereporter to the quencher prevents its fluorescence, it is only after thebreakdown of the probe that the fluorescence is detected. This processdepends on the 5′ to 3′ exonuclease activity of the polymerase used inthe PCR reaction cocktail.

Typically, the reaction is prepared as usual, with the addition of thesequence specific labeled probe the reaction commences. Afterdenaturation of the DNA the labeled probe is able to bind to itscomplementary sequence in the region of interest of the template DNA.When the PCR reaction is heated to the proper extension temperature bythe liquid metal or thermally conductive fluid block, the polymerase isactivated and DNA extension proceeds. As the polymerization continues itreaches the labeled probe bound to the complementary sequence of DNA.The polymerase breaks the RNA probe into separate nucleotides, andseparates the fluorescent reporter from the quencher. This results in anincrease in fluorescence as detected by the optical assembly. As PCRprogresses more and more of the fluorescent reporter is liberated fromits quencher, resulting in a well defined geometric increase influorescence. This allows accurate determination of the final, andinitial, quantities of DNA.

Diagnostic Use

In various applications, devices of the invention can be utilized for invitro diagnostic uses, such as detecting infectious or pathogenicagents. In one embodiment, PCR is conducted using a device of theinvention to detect various such agents, which can be any pathogenincluding without any limitation bacteria, yeast, fungi, virus,eukaryotic parasites, etc; infectious agent including influenza virus,parainfluenza virus, adenovirus, rhinovirus, coronavirus, hepatitisviruses A, B, C, D, E, etc, HIV, enterovirus, papillomavirus,coxsackievirus, herpes simplex virus, or Epstein-Barr virus; bacteriaincluding Mycobacterium, Streptococcus, Salmonella, Shigella,Staphylcococcus, Neisseria, Pseudomonads, Clostridium, or E. coli. Itwill be apparent to one of skill in the art that the PCR, sequencingreactions and related processes are readily adapted to the devices ofthe invention for use to detect any infectious agents.

One advantage of the devices of the invention is the capability toperform ultra fast PCR, which provides relatively faster times fordiagnostic purposes. For some applications (e.g., detection of biothreatagents, intra-operative diagnostic testing), rapid PCR is a benefit. Oneimportant requirement for rapid real-time PCR are a thermal cycler thatallows rapid heating, cooling, and thermal transfer, and a signalgeneration system that is compatible with the short cycle timesassociated with fast PCR. As described herein, the thermal cyclers ofthe invention can provide rapid cooling (e.g., 5-17° C./second) andrapid heating (e.g., 10-44° C./second). For example, the devices of theinvention can provided cycle times as low as about 2 seconds if desired.

Furthermore, such ultra fast PCR processes can be conducted by couplingthe devices of the invention with reagents known in the art tofacilitate faster results, in both amplification and time required toproduce a detectable signal. Such reagents are known in the art, such asdisclosed in U.S. Patent Application No. 2005/0164219. One of these thatwe have used is a faster polymerase such as KOD.

For example, specialized labeled primers can provide signal generationthat is instantaneous (U.S. Patent Application No. 2005/0164219). Areaction that is extended in the previous cycle undergoes an internalrearrangement, and as soon as the extension temperature is reached, thesignal is generated. In a standard PCR reaction with slow cyclingconditions, this signal generation difference is not significant.However, when the extension times are reduced in rapid PCR, this featurebecomes an advantage and translates into fast PCR. With the devices ofthe invention a single-copy bacterial sequences may be detected in lessthan 15 minutes. One example is the rapid detection of low levels ofBacillus spp using Scorpions primers and a fast PCR machine.Furthermore, depending on the amount of input DNA an infectious agentmay be detected in less than 10 minutes, and even low levels could bedetected in less than 14 minutes.

EXAMPLES Example 1 Stainless Steel PCR Sample Vessels

Stainless steel PCR reaction sample vessels have been demonstrated as asuitable vessels in which to conduct polymerase chain reactions. Thevessels used for initial tests were manufactured from stainless steeltubes with a final outer diameter of 0.061 inches. A two-inch length ofsample vessel was closed at one end with a press-fit stainless steelplug.

Identical 20 μL preparations for real time polymerase chain reactionsusing SYBR Green intercalating dye as an indicator were placed both in acommercial glass PCR capillary tube and in the metal sample vesseldescribed above. The reagents were then sealed from outside air byfloating 20 μL of mineral oil as an upper fluid layer in each vessel.These vessels were temperature cycled together in a commercial real-timePCR machine for 40 cycles, after which the contents of the metal samplevessel were transferred to a commercial glass PCR capillary tube. Amelting curve was run on both samples, and the results indicate that PCRproceeded successfully in both the glass and metal vessels FIG. 12.

Example 2 Realtime PCR

The liquid metal or thermally conductive fluid heat block is well suitedfor real time PCR reactions because of the fast temperature ramping,thermal uniformity and reflectivity of the liquid metal or thermallyconductive fluid.

Sample vessels are prepared by placing PCR reaction components into thesample vessels and sealing the vessels to prevent spillage orcross-contamination. The reaction components include buffer, targetnucleic acid, appropriate primers and probes, nucleotides, polymerases,as well as optional additional components. In one embodiment, fourfluorescent probes are included, each adapted to detect a differenttarget sequence, and a particular reaction vessel may include any one ormore of the fluorescent probes. Each probe advantageously responds tolight of a different incident wavelength and emits light of a differentwavelength.

A detection module is mounted above the heat block. The detection moduleincludes four detection channels. Each channel is optimized for adifferent one of the fluorescent probes included in sample vessels. Thesample vessels are placed into the heat block receptacle wells. The lidassembly is closed and positioned over the heat block

Each channel of detection module is calibrated. Calibration is performedby operating stepper motors to position the detection module such thatat least one of its channels is in optical communication with acalibration location. Each calibration location provides a knownfluorescent response. Accordingly, calibration measurements can be usedto correct subsequent sample measurements for variations or fluctuationsin detector response. Numerous calibration techniques are known in theart. When a detection module with multiple channels is used, eachchannel may be independently calibrated.

A PCR cycle is performed. The thermal cycler controls the liquid metalor thermally conductive fluid heat block to regulate the temperature ofthe sample vessels thereby holding the sample vessels at desiredtemperatures for desired lengths of time to complete a two-step orthree-step PCR cycle. The optical assembly scans and interrogates thesample vessels. The LED or other light source (such as a laser) for eachchannel is activated (flashed on for a brief period) to stimulatefluorescence. In one embodiment, the LEDs of different channels areoperated in parallel; in an alternative embodiment, they are operatedsequentially so as to avoid reflected LED light from one channel causingfalse signals in the photo detector of another channel. The operation ofoptical assembly may be controlled by an external computer or by acontroller built into the thermal cycler. The measurements aresynchronized with the operation of the thermal cycler, so thatmeasurements are identifiable as corresponding to particular times inthe PCR process. In another embodiment a controller component of thethermal cylcer may automatically turn on and off one or more fans thatare optionally attached to the thermal cycler or coupled to one or moreheat sinks.

The resulting fluorescence is detected by the corresponding photodiodeor other detector of the channel, which is read out to the externalcomputer. The detectors may be read out in various ways. For instance, apeak signal may be detected, the signal may be integrated over a timeinterval, or the decay of the fluorescent signal after the LED has beendeactivated may be measured.

These steps are repeated with the position of the detection module beingchanged each time so that each channel of detection module eventuallyinterrogates each of the sample vessels. In one embodiment, scanning andinterrogating four channels for each of 96 sample wells takes about 15seconds. The external computer may execute a program that enables a userto view measurement data as they are collected, in graphical and/ortabular form.

The real-time fluorescence measurements from process are used to detectand quantify the presence of each target sequence. Such measurements mayalso be used for purposes such as determining reaction rates andadjusting reaction parameters for improved efficiency, as well asdetermining when additional reaction cycles are no longer needed in aparticular experiment (e.g., when a sufficient quantity of a targetsequence has been produced).

It will be appreciated that process is illustrative and that variationsand modifications are possible. Steps described as sequential may beexecuted in parallel, order of steps may be varied, and steps may bemodified or combined. For example, fluorescence measurements may beperformed at any point during a PCR cycle, performed multiple timesduring each PCR cycle (including substantially continuous scanning ofthe sample wells), or not performed until after some number of PCRcycles. Any number of distinguishable fluorescent probes may be used ina single reaction vessel, and the detection module may be adapted toinclude at least as many channels as the number of probes in use. Insome embodiments, the detection module includes multiple channelsoptimized for the same probe. This may reduce the scanning time sinceonly one of these channels needs to be used to interrogate a particularsample well.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

1. A method for performing nucleic acid amplification reactions,comprising: a. providing at least two sample vessels, each of the atleast two sample vessels comprising a reaction mixture comprising apolynucleotide sample, reagents for carrying out nucleic acidamplification, and a dye for detecting amplification; b. cycling thetemperature of the reaction mixture in the at least two sample vesselsto perform multiple amplification cycles, wherein the at least twosample vessels are each in thermal contact with an oil contained withina heat block wherein the oil is actively mixed; c. regulating thetemperature of the reaction mixture in each of the sample vessels byheating and cooling a heating element in contact with a bottom surfaceof the heat block; wherein the temperature between the two samplevessels has a variance of less than +/−0.3° C.; and d. opticallymeasuring the dye between or during each of the multiple amplificationcycles to determine a level of amplification while the at least twosample vessels remain in thermal contact with the oil.
 2. The method ofclaim 1, wherein the temperature between any two sample vessels has avariance of less than +/−0.2° C.
 3. The method of claim 1, wherein thetemperature between any two sample vessels has a variance of less than+/−0.1° C.
 4. The method of claim 1 wherein the nucleic acidamplification reactions comprise PCR reactions.
 5. The method of claim 4wherein the PCR reactions comprise real time PCR (RT-PCR).
 6. The methodof claim 5 wherein the real time PCR reactions comprise quantitativereal time PCR (QRT-PCR) to simultaneously quantify and amplify aspecific portion of the polynucleotide sample.
 7. The method of claim 1wherein the multiple amplification cycles comprise either two steptemperature cycles or three step temperature cycles.
 8. The method ofclaim 1 wherein the dye for detecting the level of amplificationcomprise a fluorescent DNA-binding dye.
 9. The method of claim 1 whereinthe dye for detecting the level of amplification comprises a FRET-basedprobe.
 10. The method of claim 1 wherein the dye for detecting the levelof amplification is from a fluorescent oligonucleotide probe comprisinga fluor and a quencher.
 11. A method for detecting the presence of apathogen or an infectious agent comprising performing the method ofclaim 1 wherein the polynucleotide sample is derived from a pathogen oran infectious agent.
 12. The method of claim 11 wherein the pathogencomprises a bacteria, yeast, fungi, virus, or eukaryotic parasite. 13.The method of claim 11 wherein the infectious agent comprises influenzavirus, parainfluenza virus, adenovirus, rhinovirus, coronavirus,hepatitis viruses A, B, C, D, or E, HIV, enterovirus, papillomavirus,coxsackievirus, herpes simplex virus, Epstein-Barr virus, Mycobacterium,Streptococcus, Salmonella, Shigella, Staphylcococcus, Neisseria,Pseudomonads, Clostidium, or E. coli.
 14. The method of claim 1 whereinthe oil is actively mixed with a pump.
 15. The method of claim 1 whereinthe oil is actively mixed using a stir bar.
 16. The method of claim 15wherein the stir bar is a horizontal stir bar.
 17. The method of claim15 wherein the stir bar is a fan shaped stir bar.
 18. The method ofclaim 15 wherein the stir bar has multiple projections.
 19. The methodof claim 15 wherein the stir bar is magnetically responsive.
 20. Themethod of claim 15 wherein the stir bar is mechanically connected to amotor.
 21. The method of claim 1 wherein the oil is actively mixed usingmore than one stir bar.
 22. The method of claim 1 wherein the at leasttwo sample vessels comprise a plate.
 23. The method of claim 22 whereinthe number of sample vessels in the plate are 6, 12, 16, 24, 48, 96, or384.
 24. The method of claim 1 wherein the oil comprises silicone oil orcarboxy-modified silicone oil, mineral oil, napthenic oil,hydroisomerized oil, or paraffinic oil.
 25. The method of claim 1wherein the oil comprises a hydrocarbon compound.